added diamond support, added ref weight support to heuristic and bpo,…

… added tcdb

Former-commit-id: 61ad057

MANTIS.config

@@ -5,28 +5,30 @@
 
 #######DEFAULT PATHS#######
 #You can add custom paths here, otherwise they will be set to default values
-#ncbi_dmp_path_folder=
-#default_hmms_folder=
-#####<custom_hmms_folder> defines the folder where Mantis will look for MULTIPLE custom HMMs. Each HMM should be contained within a folder, such that the path will look something like this: /path/to/custom_hmms_folder/custom1/custom1.hmm
-#custom_hmms_folder=
+#ncbi_resources_folder=
+#default_ref_folder=
+#####<custom_ref_folder> defines the folder where Mantis will look for MULTIPLE custom HMMs or DMND. Each HMM should be contained within a folder, such that the path will look something like this: /path/to/custom_ref_folder/custom1/custom1.hmm
+#custom_ref_folder=
 #nog_hmm_folder=
 #pfam_hmm_folder=
 #kofam_hmm_folder=
 #ncbi_hmm_folder=
 #tigrfam_hmm_folder=
+tcdb_seq_folder=NA
 #nog_tax=NCBI_ID
 
 #####Make sure the  names of the weights correspond to the path of the hmms
 #####example: <NOGT>_hmm_folder should be <NOGT>_weight
-#####example: custom_hmm=path/to/customHMM.hmm should be customHMM_weight
+#####example: custom_ref=path/to/customHMM.hmm should be customHMM_weight
 nog_weight=0.8
 pfam_weight=0.9
 tigrfam_weight=0.5
 
 
-#######CUSTOM HMMS#######
-#####<custom_hmm> defines the folder or file where Mantis will look for a SINGLE custom HMM. The path will look something like this: /path/to/custom1/custom1.hmm or /path/to/custom1/
-#custom_hmm=path/to/hmm/custom1.hmm
+#######CUSTOM REFERENCES#######
+#####<custom_ref> defines the folder or file where Mantis will look for a SINGLE custom reference (HMM or DMND). The path will look something like this: /path/to/custom1/custom1.hmm or /path/to/custom1/
+#custom_ref=path/to/hmm/custom1.hmm
+#custom_ref=path/to/hmm/custom2.dmnd
 #to set the weight, simply add a line with the hmm file name followed by _weight , like so:
 #custom1_weight=0.5
 

References/Custom_references/readme.md

@@ -0,0 +1,10 @@
+Custom references will go here
+
+Please use one folder per source otherwise it won't be recognized.
+
+If using a HMM, please use hmmpress on the hmm within each folder.
+If using sequences, use Diamond to create a Diamond database.
+
+example1.tar.gz contains an example custom hmm source.
+
+You can also use the function ```merge_hmm_folder``` to merge a target folder with hmms. This function will merge all hmms into one global hmm and then press it.

__main__.py

@@ -62,6 +62,9 @@
                              '\t\t\ttaxon name, e.g. "Proteobacteria" or "Escherichia coli"\n'
                              '\t\t\tNCBI taxon ID, e.g.: 561 for Escherichia coli\n'
                              'Providing NCBI IDs is faster and safer.')
+    parser.add_argument('-gc', '--genetic_code',
+                        help='[optional]\tIf you want Mantis to translate your target fasta, please provide a genetic code. Default is 11. \n'
+                             '\t\tFor further details please see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes\n')
     parser.add_argument('-k', '--keep_files', action='store_true',
                         help='[optional]\tKeep intermediary output files')
     parser.add_argument('-sc', '--skip_consensus', action='store_true',
@@ -113,6 +116,7 @@
         overlap_value = args.overlap_value
         minimum_consensus_overlap = args.minimum_consensus_overlap
         organism_details = args.organism_details
+        genetic_code = args.genetic_code
         domain_algorithm = args.domain_algorithm
         best_combo_formula = args.best_combo_formula
         sorting_type = args.sorting_type
@@ -150,6 +154,7 @@
                            overlap_value=overlap_value,
                            minimum_consensus_overlap=minimum_consensus_overlap,
                            organism_details=organism_details,
+                           genetic_code=genetic_code,
                            domain_algorithm=domain_algorithm,
                            best_combo_formula=best_combo_formula,
                            sorting_type=sorting_type,
@@ -175,7 +180,8 @@
         mantis_config = args.mantis_config
         force_download = args.force_download
         chunk_size = args.chunk_size
-        setup_databases(force_download=force_download, chunk_size=chunk_size, mantis_config=mantis_config)
+        cores = args.cores
+        setup_databases(force_download=force_download, chunk_size=chunk_size, mantis_config=mantis_config,cores=cores)
     elif args.execution_type == 'merge_hmm_folder':
         target = args.target
         merge_hmm_folder(target_folder=target)

source/Exceptions.py

@@ -1,3 +1,12 @@
+RequirementsNotMet='Installation check not passed! Make sure you\'ve setup the databases and your system meets all the requirements!'
+NoValidFiles='No valid files to annotate'
+InvalidTargetFile='You did not insert a valid target file!\n'
+InstallationCheckNotPassed='Installation check not passed! Make sure you\'ve setup the databases and your system meets all the requirements!'
+CythonNotCompiled= 'Cython has not been correctly compiled! Please go to mantis/source/ and run python utils.py'
+BadNumberWorkers='You should not be seeing this, please contact the developer. Invalid number of workers in '
+ConnectionError='Could not connect to url:\n'
+InvalidTranslation='Invalid residues for translation. Please make sure you provided a CDS of DNA or RNA in the target file:\n'
+
 class RequirementsNotMet(Exception):
     def __init__(self, *args):
         if args:
@@ -14,30 +23,3 @@ def __str__(self):
             return 'Requirements not met'
 
 
-class MissingCondaEnvironment(Exception):
-    def __str__(self):
-        return 'Conda environment is missing from configuration file!'
-
-
-class InvalidFunction(Exception):
-    def __str__(self):
-        return 'This function is not available in this module!'
-
-
-class InvalidTargetFile(Exception):
-    def __str__(self):
-        return 'You did not insert a valid target file!'
-
-
-class InstallationCheckNotPassed(Exception):
-    def __str__(self):
-        return 'Installation check not passed! Make sure you\'ve setup the databases and your system meets all the requirements!'
-
-
-class CythonNotCompiled(Exception):
-    def __str__(self):
-        return 'Cython has not been correctly compiled! Please go to mantis/source/ and run python utils.py'
-
-class BadNumberWorkers(Exception):
-    def __str__(self):
-        return 'Number of workers not correctly defined. You should not be seeing this! Contact developer!'