iML1515_GP - Creating the GEM-PRO.ipynb

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   "source": [
    "# Creating the GEM-PRO"
   ]
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   "source": [
    "import sys\n",
    "import logging\n",
    "import os.path as op\n",
    "import pandas as pd\n",
    "from ssbio.pipeline.gempro import GEMPRO\n",
    "\n",
    "logger = logging.getLogger()\n",
    "logger.setLevel(logging.INFO)\n",
    "handler = logging.StreamHandler(sys.stderr)\n",
    "formatter = logging.Formatter('[%(asctime)s] [%(name)s] %(levelname)s: %(message)s', datefmt=\"%Y-%m-%d %H:%M\")\n",
    "handler.setFormatter(formatter)\n",
    "logger.handlers = [handler]"
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   "source": [
    "# Printing multiple outputs per cell\n",
    "from IPython.core.interactiveshell import InteractiveShell\n",
    "InteractiveShell.ast_node_interactivity = \"all\""
   ]
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   "source": [
    "# Specify the folders and model\n",
    "GEM_NAME = 'iML1515_GP'\n",
    "ROOT_DIR = '.'\n",
    "GEM_FILE = 'iML1515_GP/model/iML1515.json'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
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   "outputs": [
    {
     "name": "stderr",
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     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Creating GEM-PRO project directory in folder .\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: ./iML1515_GP: GEM-PRO project location\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: iML1515: loaded model\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 2719: number of reactions\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 2229: number of reactions linked to a gene\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 1515: number of genes (excluding spontaneous)\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 1919: number of metabolites\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] WARNING: IMPORTANT: All Gene objects have been transformed into GenePro objects, and will be for any new ones\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 1516: number of genes\n"
     ]
    }
   ],
   "source": [
    "# Create the GEM-PRO project\n",
    "my_gempro = GEMPRO(gem_name=GEM_NAME, root_dir=ROOT_DIR, gem_file_path=GEM_FILE, gem_file_type='json', pdb_file_type='mmtf')"
   ]
  },
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     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 1513/1516: number of genes mapped to KEGG\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Completed ID mapping --> KEGG. See the \"df_kegg_metadata\" attribute for a summary dataframe.\n"
     ]
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     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 1514/1516: number of genes mapped to UniProt\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Completed ID mapping --> UniProt. See the \"df_uniprot_metadata\" attribute for a summary dataframe.\n"
     ]
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     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] ERROR: b4104, P16683: unable to complete web request\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "HTTP Error 300: \n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Completed manual ID mapping --> UniProt. See the \"df_uniprot_metadata\" attribute for a summary dataframe.\n"
     ]
    },
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     "text": [
      "[2019-10-17 16:12] [ssbio.core.protein] ERROR: b4104: no sequences mapped\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 1515/1516: number of genes with a representative sequence\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: See the \"df_representative_sequences\" attribute for a summary dataframe.\n"
     ]
    }
   ],
   "source": [
    "my_gempro.kegg_mapping_and_metadata(kegg_organism_code='eco')\n",
    "my_gempro.uniprot_mapping_and_metadata(model_gene_source='ENSEMBLGENOME_ID')\n",
    "my_gempro.manual_uniprot_mapping({'b4104':'P16683', 'b2092':'P69831'})\n",
    "my_gempro.set_representative_sequence()"
   ]
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   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Mapping UniProt IDs --> PDB IDs...\n"
     ]
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     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 705/1516: number of genes with at least one experimental structure\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Completed UniProt --> best PDB mapping. See the \"df_pdb_ranking\" attribute for a summary dataframe.\n"
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     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Completed sequence --> PDB BLAST. See the \"df_pdb_blast\" attribute for a summary dataframe.\n",
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: 17: number of genes with additional structures added from BLAST\n"
     ]
    }
   ],
   "source": [
    "my_gempro.map_uniprot_to_pdb()\n",
    "my_gempro.blast_seqs_to_pdb(seq_ident_cutoff=.98, all_genes=False)"
   ]
  },
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      "\n"
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     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Updated homology model information for 1512 genes.\n"
     ]
    }
   ],
   "source": [
    "# Creating manual mapping dictionary for ECOLI I-TASSER models\n",
    "homology_models = '/home/nathan/projects_archive/homology_models/ECOLI/zhang/'\n",
    "homology_models_df = pd.read_csv('/home/nathan/projects_archive/homology_models/ECOLI/zhang_data/160804-ZHANG_INFO.csv')\n",
    "tmp = homology_models_df[['zhang_id','model_file','m_gene']].drop_duplicates()\n",
    "tmp = tmp[pd.notnull(tmp.m_gene)]\n",
    "\n",
    "homology_model_dict = {}\n",
    "\n",
    "for i,r in tmp.iterrows():\n",
    "    homology_model_dict[r['m_gene']] = {r['zhang_id']: {'model_file':op.join(homology_models, r['model_file']),\n",
    "                                                        'file_type':'pdb'}}\n",
    "    \n",
    "my_gempro.get_manual_homology_models(homology_model_dict)"
   ]
  },
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      "\n"
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     "output_type": "stream",
     "text": [
      "[2019-10-17 16:12] [ssbio.pipeline.gempro] INFO: Updated homology model information for 1412 genes.\n"
     ]
    }
   ],
   "source": [
    "# Creating manual mapping dictionary for ECOLI SUNPRO models\n",
    "homology_models = '/home/nathan/projects_archive/homology_models/ECOLI/sunpro/'\n",
    "homology_models_df = pd.read_csv('/home/nathan/projects_archive/homology_models/ECOLI/sunpro_data/160609-SUNPRO_INFO.csv')\n",
    "tmp = homology_models_df[['sunpro_id','model_file','m_gene']].drop_duplicates()\n",
    "tmp = tmp[pd.notnull(tmp.m_gene)]\n",
    "\n",
    "homology_model_dict = {}\n",
    "\n",
    "for i,r in tmp.iterrows():\n",
    "    homology_model_dict[r['m_gene']] = {r['sunpro_id']: {'model_file':op.join(homology_models, r['model_file']),\n",
    "                                                         'file_type':'pdb'}}\n",
    "    \n",
    "my_gempro.get_manual_homology_models(homology_model_dict)"
   ]
  },
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      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "[2019-10-17 16:14] [ssbio.core.protein] ERROR: Protein b2668, PDB 5hbo: unable to parse structure file as mmtf. Falling back to mmCIF format.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(' ', 63, ' ') defined twice\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "[2019-10-17 16:15] [ssbio.core.protein] ERROR: Protein b1101, PDB 1o2f: unable to parse structure file as mmtf. Falling back to mmCIF format.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "[2019-10-17 16:15] [ssbio.core.protein] ERROR: Protein b1817, PDB 1vrc: unable to parse structure file as mmtf. Falling back to mmCIF format.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "8\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "[2019-10-17 16:16] [ssbio.core.protein] ERROR: Protein b3599, PDB 1j6t: unable to parse structure file as mmtf. Falling back to mmCIF format.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:426 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:427 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:485 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n",
      "/mnt/projects/ssbio/ssbio/protein/sequence/utils/alignment.py:486 FutureWarning: \n",
      ".ix is deprecated. Please use\n",
      ".loc for label based indexing or\n",
      ".iloc for positional indexing\n",
      "\n",
      "See the documentation here:\n",
      "http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:19] [ssbio.pipeline.gempro] INFO: 1513/1516: number of genes with a representative structure\n",
      "[2019-10-17 16:19] [ssbio.pipeline.gempro] INFO: See the \"df_representative_structures\" attribute for a summary dataframe.\n"
     ]
    }
   ],
   "source": [
    "my_gempro.set_representative_structure()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "1aa8a5e003424",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "source": [
    "# Adding domain information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "14394e8b8fe28",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "domains = pd.read_csv('iML1515_GP/data/iML1515_domains.csv', index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "09eb5c0ef5605",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    },
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>fatcat_domain</th>\n",
       "      <th>u_uniprot_acc</th>\n",
       "      <th>pdb</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>d1hqsa_</td>\n",
       "      <td>P08200</td>\n",
       "      <td>1AI2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>d1hqsa_</td>\n",
       "      <td>P08200</td>\n",
       "      <td>1AI3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>d1hqsa_</td>\n",
       "      <td>P08200</td>\n",
       "      <td>1BL5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>d1hqsa_</td>\n",
       "      <td>P08200</td>\n",
       "      <td>1CW1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>d1hqsa_</td>\n",
       "      <td>P08200</td>\n",
       "      <td>1CW4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  fatcat_domain u_uniprot_acc   pdb\n",
       "0       d1hqsa_        P08200  1AI2\n",
       "1       d1hqsa_        P08200  1AI3\n",
       "2       d1hqsa_        P08200  1BL5\n",
       "3       d1hqsa_        P08200  1CW1\n",
       "4       d1hqsa_        P08200  1CW4"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "domains.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "9e4a2d073062d",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "for g in my_gempro.genes_with_a_representative_sequence:\n",
    "    for s in g.protein.sequences:\n",
    "        if s.uniprot in domains.u_uniprot_acc.tolist():\n",
    "            s.domains = domains[domains.u_uniprot_acc == s.uniprot]['fatcat_domain'].unique().tolist()\n",
    "        else:\n",
    "            s.domains = None\n",
    "    \n",
    "    if g.protein.representative_sequence.uniprot in domains.u_uniprot_acc.tolist():\n",
    "        g.protein.representative_sequence.domains = domains[domains.u_uniprot_acc == s.uniprot]['fatcat_domain'].unique().tolist()\n",
    "    else:\n",
    "        g.protein.representative_sequence.domains = None\n",
    "        \n",
    "    for t in g.protein.structures:\n",
    "        if t.is_experimental:\n",
    "            if t.id.upper() in domains.pdb.tolist():\n",
    "                t.domains = domains[domains.pdb == t.id.upper()]['fatcat_domain'].unique().tolist()\n",
    "            else:\n",
    "                t.domains = None\n",
    "        else:\n",
    "            t.domains = None\n",
    "    \n",
    "    if g.protein.representative_structure:\n",
    "        if g.protein.representative_structure.is_experimental:\n",
    "            if g.protein.representative_structure.original_structure_id.upper() in domains.pdb.tolist():\n",
    "                g.protein.representative_structure.domains = domains[domains.pdb == g.protein.representative_structure.original_structure_id.upper()]['fatcat_domain'].unique().tolist()\n",
    "            else:\n",
    "                g.protein.representative_structure.domains = None\n",
    "        else:\n",
    "            g.protein.representative_structure.domains = None"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "413641ad2ef6a",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "source": [
    "# Saving"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "d0ba401f8c863",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[2019-10-17 16:19] [root] WARNING: json-tricks: numpy scalar serialization is experimental and may work differently in future versions\n",
      "[2019-10-17 16:19] [ssbio.io] INFO: Saved <class 'ssbio.pipeline.gempro.GEMPRO'> (id: iML1515_GP) to /home/nathan/projects/iML1515_GP/iML1515_GP/model/iML1515_GP.json\n"
     ]
    }
   ],
   "source": [
    "my_gempro.save_json('iML1515_GP/model/iML1515_GP.json', compression=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "2c7929fbed5",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "my_gempro.save_pickle(outfile='iML1515_GP/model/iML1515_GP.pckl')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "41c9a6d90a615",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "source": [
    "# Recreating the original dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "0a9aa3f997912",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/nathan/anaconda3/lib/python3.7/site-packages/pandas/core/frame.py:7123 FutureWarning: Sorting because non-concatenation axis is not aligned. A future version\n",
      "of pandas will change to not sort by default.\n",
      "\n",
      "To accept the future behavior, pass 'sort=False'.\n",
      "\n",
      "To retain the current behavior and silence the warning, pass 'sort=True'.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "df_uniprot = my_gempro.df_uniprot_metadata\n",
    "df_kegg = my_gempro.df_kegg_metadata\n",
    "df_repseq = my_gempro.df_representative_sequences\n",
    "df_pdbblast = my_gempro.df_pdb_blast\n",
    "df_pdbrank = my_gempro.df_pdb_ranking\n",
    "df_repstruct = my_gempro.df_representative_structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "f4a01fe46b807",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "logger.setLevel(logging.CRITICAL)\n",
    "df_pdbmetadata = my_gempro.df_pdb_metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "7c33070413887",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "it_homology_models_df = pd.read_csv('/home/nathan/projects_archive/homology_models/ECOLI/zhang_data/160804-ZHANG_INFO.csv')\n",
    "sp_homology_models_df = pd.read_csv('/home/nathan/projects_archive/homology_models/ECOLI/sunpro_data/160609-SUNPRO_INFO.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "797c15e3de92a",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "pre_df = []\n",
    "df_gempro = pd.DataFrame()\n",
    "for rxn in my_gempro.model.reactions:\n",
    "    for gene in rxn.genes:\n",
    "        if gene.id == 's0001':\n",
    "            continue\n",
    "        gene_dict = {}\n",
    "        gene_dict['m_reaction'] = rxn.id\n",
    "        gene_dict['m_gene_reaction_rule'] = rxn.gene_reaction_rule\n",
    "        gene_dict['m_metabolites'] = ';'.join([x.id for x in rxn.metabolites])\n",
    "        gene_dict['m_subsystem'] = rxn.subsystem\n",
    "        gene_dict['m_gene'] = gene.id\n",
    "        \n",
    "        if my_gempro.genes.get_by_id(gene.id).protein.representative_sequence:\n",
    "            gene_dict['seq_uniprot'] = df_repseq.loc[gene.id, 'uniprot']\n",
    "            gene_dict['seq_kegg'] = df_repseq.loc[gene.id, 'kegg']\n",
    "            gene_dict['seq_mapped_pdbs'] = df_repseq.loc[gene.id, 'pdbs']\n",
    "            if my_gempro.genes.get_by_id(gene.id).protein.representative_sequence.domains:\n",
    "                gene_dict['seq_domains'] = ';'.join(my_gempro.genes.get_by_id(gene.id).protein.representative_sequence.domains)\n",
    "            gene_dict['seq_file'] = df_repseq.loc[gene.id, 'sequence_file']\n",
    "        \n",
    "        if my_gempro.genes.get_by_id(gene.id).protein.representative_structure:\n",
    "            repstruct = df_repstruct.loc[gene.id, 'id']\n",
    "            ispdb = df_repstruct.loc[gene.id, 'is_experimental']\n",
    "            gene_dict['struct_id'] = repstruct\n",
    "            gene_dict['struct_is_experimental'] = ispdb\n",
    "            gene_dict['struct_percent_seq_cov'] = gene.protein.representative_chain_seq_coverage\n",
    "            if ispdb:\n",
    "                pdb_id = repstruct.split('-')[1].lower()\n",
    "                sliced = df_pdbmetadata[df_pdbmetadata.pdb_id == pdb_id]\n",
    "                gene_dict['struct_pdb'] = sliced.loc[gene.id, 'pdb_id']\n",
    "                gene_dict['struct_resolution'] = sliced.loc[gene.id, 'resolution']\n",
    "                gene_dict['struct_chemicals'] = sliced.loc[gene.id, 'chemicals']\n",
    "                if my_gempro.genes.get_by_id(gene.id).protein.representative_structure.domains:\n",
    "                    gene_dict['struct_domains'] = ';'.join(my_gempro.genes.get_by_id(gene.id).protein.representative_structure.domains)\n",
    "            else:\n",
    "                if '_ECOLI' not in repstruct:\n",
    "                    ident = repstruct.split('-')[1]\n",
    "                    sliced = sp_homology_models_df[sp_homology_models_df.sunpro_id == ident]\n",
    "                else:\n",
    "                    ident = repstruct.split('-')[1]\n",
    "                    sliced = it_homology_models_df[it_homology_models_df.zhang_id == ident]\n",
    "                    template = sliced.i_template.values[0]\n",
    "                    gene_dict['struct_homology_template'] = template\n",
    "\n",
    "            gene_dict['struct_file'] = df_repstruct.loc[gene.id, 'structure_file']\n",
    "        \n",
    "        pre_df.append(gene_dict)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "0168c8084fb0a",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "final_df = pd.DataFrame(pre_df, columns=['m_reaction','m_gene_reaction_rule','m_metabolites','m_subsystem','m_gene','seq_uniprot','seq_kegg','seq_mapped_pdbs','seq_domains','seq_file','struct_id','struct_is_experimental','struct_percent_seq_cov','struct_pdb','struct_resolution','struct_chemicals','struct_domains','struct_homology_template','struct_file']).sort_values(by='m_reaction').reset_index(drop=True).set_index('m_reaction')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "be99118d1be0d",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [],
   "source": [
    "final_df.to_csv(op.join(my_gempro.data_dir, 'iML1515_GP.csv'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "janus": {
     "all_versions_showing": false,
     "cell_hidden": false,
     "current_version": 0,
     "id": "d565d8d528bd",
     "named_versions": [],
     "output_hidden": false,
     "show_versions": false,
     "source_hidden": false,
     "versions": []
    }
   },
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>m_gene_reaction_rule</th>\n",
       "      <th>m_metabolites</th>\n",
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       "      <td>Zn2tex</td>\n",
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       "      <td>P77747.fasta</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>1PHO</td>\n",
       "      <td>PDP:5FVNAa</td>\n",
       "      <td>P02932.fasta</td>\n",
       "      <td>REP-PHOE_ECOLI</td>\n",
       "      <td>False</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1pho</td>\n",
       "      <td>PHOE_ECOLI_model1_clean-X_clean.pdb</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4579 rows × 18 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          m_gene_reaction_rule  \\\n",
       "m_reaction                                       \n",
       "12PPDRtex   (b0241 or b0929 or b1377 or b2215)   \n",
       "12PPDRtex   (b0241 or b0929 or b1377 or b2215)   \n",
       "12PPDRtex   (b0241 or b0929 or b1377 or b2215)   \n",
       "12PPDRtex   (b0241 or b0929 or b1377 or b2215)   \n",
       "12PPDStex   (b0241 or b0929 or b1377 or b2215)   \n",
       "...                                        ...   \n",
       "ZNabcpp            (b1859 and b1858 and b1857)   \n",
       "Zn2tex      (b0241 or b0929 or b1377 or b2215)   \n",
       "Zn2tex      (b0241 or b0929 or b1377 or b2215)   \n",
       "Zn2tex      (b0241 or b0929 or b1377 or b2215)   \n",
       "Zn2tex      (b0241 or b0929 or b1377 or b2215)   \n",
       "\n",
       "                                     m_metabolites  \\\n",
       "m_reaction                                           \n",
       "12PPDRtex                    12ppd__R_e;12ppd__R_p   \n",
       "12PPDRtex                    12ppd__R_e;12ppd__R_p   \n",
       "12PPDRtex                    12ppd__R_e;12ppd__R_p   \n",
       "12PPDRtex                    12ppd__R_e;12ppd__R_p   \n",
       "12PPDStex                    12ppd__S_e;12ppd__S_p   \n",
       "...                                            ...   \n",
       "ZNabcpp     h2o_c;atp_c;zn2_p;h_c;adp_c;pi_c;zn2_c   \n",
       "Zn2tex                                 zn2_e;zn2_p   \n",
       "Zn2tex                                 zn2_e;zn2_p   \n",
       "Zn2tex                                 zn2_e;zn2_p   \n",
       "Zn2tex                                 zn2_e;zn2_p   \n",
       "\n",
       "                                       m_subsystem m_gene seq_uniprot  \\\n",
       "m_reaction                                                              \n",
       "12PPDRtex          Transport, Outer Membrane Porin  b1377      P77747   \n",
       "12PPDRtex          Transport, Outer Membrane Porin  b0241      P02932   \n",
       "12PPDRtex          Transport, Outer Membrane Porin  b0929      P02931   \n",
       "12PPDRtex          Transport, Outer Membrane Porin  b2215      P06996   \n",
       "12PPDStex          Transport, Outer Membrane Porin  b0929      P02931   \n",
       "...                                            ...    ...         ...   \n",
       "ZNabcpp     Inorganic Ion Transport and Metabolism  b1857      P39172   \n",
       "Zn2tex             Transport, Outer Membrane Porin  b0929      P02931   \n",
       "Zn2tex             Transport, Outer Membrane Porin  b2215      P06996   \n",
       "Zn2tex             Transport, Outer Membrane Porin  b1377      P77747   \n",
       "Zn2tex             Transport, Outer Membrane Porin  b0241      P02932   \n",
       "\n",
       "                        seq_kegg  \\\n",
       "m_reaction                         \n",
       "12PPDRtex   ecj:JW1371;eco:b1377   \n",
       "12PPDRtex   ecj:JW0231;eco:b0241   \n",
       "12PPDRtex   ecj:JW0912;eco:b0929   \n",
       "12PPDRtex   ecj:JW2203;eco:b2215   \n",
       "12PPDStex   ecj:JW0912;eco:b0929   \n",
       "...                          ...   \n",
       "ZNabcpp     ecj:JW5831;eco:b1857   \n",
       "Zn2tex      ecj:JW0912;eco:b0929   \n",
       "Zn2tex      ecj:JW2203;eco:b2215   \n",
       "Zn2tex      ecj:JW1371;eco:b1377   \n",
       "Zn2tex      ecj:JW0231;eco:b0241   \n",
       "\n",
       "                                              seq_mapped_pdbs  \\\n",
       "m_reaction                                                      \n",
       "12PPDRtex                                                 NaN   \n",
       "12PPDRtex                                                1PHO   \n",
       "12PPDRtex   1BT9;1GFM;1GFN;1GFO;1GFP;1GFQ;1HXT;1HXU;1HXX;1...   \n",
       "12PPDRtex                                 2J1N;2J4U;2ZLE;4A8D   \n",
       "12PPDStex   1BT9;1GFM;1GFN;1GFO;1GFP;1GFQ;1HXT;1HXU;1HXX;1...   \n",
       "...                                                       ...   \n",
       "ZNabcpp                         2OGW;2OSV;2PRS;2PS0;2PS3;2PS9   \n",
       "Zn2tex      1BT9;1GFM;1GFN;1GFO;1GFP;1GFQ;1HXT;1HXU;1HXX;1...   \n",
       "Zn2tex                                    2J1N;2J4U;2ZLE;4A8D   \n",
       "Zn2tex                                                    NaN   \n",
       "Zn2tex                                                   1PHO   \n",
       "\n",
       "                      seq_domains      seq_file       struct_id  \\\n",
       "m_reaction                                                        \n",
       "12PPDRtex                     NaN  P77747.fasta  REP-OMPN_ECOLI   \n",
       "12PPDRtex              PDP:5FVNAa  P02932.fasta  REP-PHOE_ECOLI   \n",
       "12PPDRtex              PDP:5FVNAa  P02931.fasta        REP-2zfg   \n",
       "12PPDRtex              PDP:5FVNAa  P06996.fasta        REP-2j1n   \n",
       "12PPDStex              PDP:5FVNAa  P02931.fasta        REP-2zfg   \n",
       "...                           ...           ...             ...   \n",
       "ZNabcpp     PDP:2OSVAa;PDP:2OSVAb  P39172.fasta        REP-2prs   \n",
       "Zn2tex                 PDP:5FVNAa  P02931.fasta        REP-2zfg   \n",
       "Zn2tex                 PDP:5FVNAa  P06996.fasta        REP-2j1n   \n",
       "Zn2tex                        NaN  P77747.fasta  REP-OMPN_ECOLI   \n",
       "Zn2tex                 PDP:5FVNAa  P02932.fasta  REP-PHOE_ECOLI   \n",
       "\n",
       "           struct_is_experimental  struct_percent_seq_cov struct_pdb  \\\n",
       "m_reaction                                                             \n",
       "12PPDRtex                   False                1.000000        NaN   \n",
       "12PPDRtex                   False                1.000000        NaN   \n",
       "12PPDRtex                    True                0.936464       2zfg   \n",
       "12PPDRtex                    True                0.942779       2j1n   \n",
       "12PPDStex                    True                0.936464       2zfg   \n",
       "...                           ...                     ...        ...   \n",
       "ZNabcpp                      True                0.848387       2prs   \n",
       "Zn2tex                       True                0.936464       2zfg   \n",
       "Zn2tex                       True                0.942779       2j1n   \n",
       "Zn2tex                      False                1.000000        NaN   \n",
       "Zn2tex                      False                1.000000        NaN   \n",
       "\n",
       "            struct_resolution struct_chemicals         struct_domains  \\\n",
       "m_reaction                                                              \n",
       "12PPDRtex                 NaN              NaN                    NaN   \n",
       "12PPDRtex                 NaN              NaN                    NaN   \n",
       "12PPDRtex                1.59           MG;C8E             PDP:5FVNAa   \n",
       "12PPDRtex                2.00        CL;MG;D12             PDP:5FVNAa   \n",
       "12PPDStex                1.59           MG;C8E             PDP:5FVNAa   \n",
       "...                       ...              ...                    ...   \n",
       "ZNabcpp                  1.70           ZN;IPA  PDP:2OSVAa;PDP:2OSVAb   \n",
       "Zn2tex                   1.59           MG;C8E             PDP:5FVNAa   \n",
       "Zn2tex                   2.00        CL;MG;D12             PDP:5FVNAa   \n",
       "Zn2tex                    NaN              NaN                    NaN   \n",
       "Zn2tex                    NaN              NaN                    NaN   \n",
       "\n",
       "           struct_homology_template                          struct_file  \n",
       "m_reaction                                                                \n",
       "12PPDRtex                      2ixx  OMPN_ECOLI_model1_clean-X_clean.pdb  \n",
       "12PPDRtex                      1pho  PHOE_ECOLI_model1_clean-X_clean.pdb  \n",
       "12PPDRtex                       NaN                     2zfg-A_clean.pdb  \n",
       "12PPDRtex                       NaN                     2j1n-A_clean.pdb  \n",
       "12PPDStex                       NaN                     2zfg-A_clean.pdb  \n",
       "...                             ...                                  ...  \n",
       "ZNabcpp                         NaN                     2prs-A_clean.pdb  \n",
       "Zn2tex                          NaN                     2zfg-A_clean.pdb  \n",
       "Zn2tex                          NaN                     2j1n-A_clean.pdb  \n",
       "Zn2tex                         2ixx  OMPN_ECOLI_model1_clean-X_clean.pdb  \n",
       "Zn2tex                         1pho  PHOE_ECOLI_model1_clean-X_clean.pdb  \n",
       "\n",
       "[4579 rows x 18 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
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