NCBI_NLM_Codeathon_Query_Tool.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "AGvtzLVm-StK",
        "outputId": "a2041b38-2c45-4e05-c3df-3e15c82d3c33"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Collecting Bio\n",
            "  Downloading bio-1.6.2-py3-none-any.whl (278 kB)\n",
            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m278.6/278.6 kB\u001b[0m \u001b[31m2.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hCollecting biopython>=1.80 (from Bio)\n",
            "  Downloading biopython-1.83-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)\n",
            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.1/3.1 MB\u001b[0m \u001b[31m18.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hRequirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (from Bio) (2.31.0)\n",
            "Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from Bio) (4.66.2)\n",
            "Collecting mygene (from Bio)\n",
            "  Downloading mygene-3.2.2-py2.py3-none-any.whl (5.4 kB)\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from Bio) (1.5.3)\n",
            "Requirement already satisfied: pooch in /usr/local/lib/python3.10/dist-packages (from Bio) (1.8.0)\n",
            "Collecting gprofiler-official (from Bio)\n",
            "  Downloading gprofiler_official-1.0.0-py3-none-any.whl (9.3 kB)\n",
            "Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython>=1.80->Bio) (1.25.2)\n",
            "Collecting biothings-client>=0.2.6 (from mygene->Bio)\n",
            "  Downloading biothings_client-0.3.1-py2.py3-none-any.whl (29 kB)\n",
            "Requirement already satisfied: python-dateutil>=2.8.1 in /usr/local/lib/python3.10/dist-packages (from pandas->Bio) (2.8.2)\n",
            "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->Bio) (2023.4)\n",
            "Requirement already satisfied: platformdirs>=2.5.0 in /usr/local/lib/python3.10/dist-packages (from pooch->Bio) (4.2.0)\n",
            "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from pooch->Bio) (23.2)\n",
            "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests->Bio) (3.3.2)\n",
            "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests->Bio) (3.6)\n",
            "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests->Bio) (2.0.7)\n",
            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests->Bio) (2024.2.2)\n",
            "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.8.1->pandas->Bio) (1.16.0)\n",
            "Installing collected packages: biopython, gprofiler-official, biothings-client, mygene, Bio\n",
            "Successfully installed Bio-1.6.2 biopython-1.83 biothings-client-0.3.1 gprofiler-official-1.0.0 mygene-3.2.2\n"
          ]
        }
      ],
      "source": [
        "!pip install Bio\n",
        "\n",
        "from Bio import Entrez, SeqIO\n",
        "from io import StringIO, BytesIO\n",
        "import xml.etree.ElementTree as ET\n",
        "import re\n",
        "import ast\n",
        "import json\n",
        "import time\n",
        "import os\n",
        "\n",
        "\n",
        "Entrez.email = 'hari.parthasarathy@berkeley.edu'  # Replace with your email address\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def search_sra(query, count):\n",
        "\n",
        "    handle = Entrez.esearch(db = 'sra', term = query, retmax = count)\n",
        "    records = Entrez.read(handle)\n",
        "    handle.close()\n",
        "\n",
        "    id_list = records['IdList']\n",
        "\n",
        "    for record_id in id_list:\n",
        "        summary = Entrez.esummary(db = 'sra', id = record_id)\n",
        "        read_summary = Entrez.read(summary)\n",
        "        data = read_summary[0]\n",
        "        summary.close()\n",
        "\n",
        "        print('Metadata ', data)\n",
        "        print('\\n')\n",
        "\n",
        "        print('RecordID: ',record_id)\n",
        "        print('\\n')\n"
      ],
      "metadata": {
        "id": "Ssw1KJHI-WyK"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "search_sra(\"PRJDB9292\", 1)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "QUQ0_Jg8EhP-",
        "outputId": "5a59b27e-8346-40be-b77b-48f89945f6cb"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Metadata  {'Item': [], 'Id': '19702229', 'ExpXml': '<Summary><Title>Illumina MiSeq paired end sequencing of SAMD00204524</Title><Platform instrument_model=\"Illumina MiSeq\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"370845\" total_bases=\"223248690\" total_size=\"121576221\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"DRA009581\" center_name=\"KURUME_U\" contact_name=\"Biostatistics Center, Kurume University\" lab_name=\"Biostatistics Center, Kurume University\"/><Experiment acc=\"DRX197985\" ver=\"1\" status=\"public\" name=\"Illumina MiSeq paired end sequencing of SAMD00204524\"/><Study acc=\"DRP008133\" name=\"Gut metagenome analysis, Parkinsons disease and history of appendectomy\"/><Organism taxid=\"408170\" ScientificName=\"human gut metagenome\"/><Sample acc=\"DRS226459\" name=\"\"/><Instrument ILLUMINA=\"Illumina MiSeq\"/><Library_descriptor><LIBRARY_NAME>DN20</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT> <PAIRED NOMINAL_LENGTH=\"302\"/> </LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL/></Library_descriptor><Bioproject>PRJDB9292</Bioproject><Biosample>SAMD00204524</Biosample>', 'Runs': '<Run acc=\"DRR207635\" total_spots=\"370845\" total_bases=\"223248690\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/>', 'ExtLinks': '', 'CreateDate': '2022/02/01', 'UpdateDate': '2022/02/01'}\n",
            "\n",
            "\n",
            "RecordID:  19702229\n",
            "\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def request_gene_id(query, count, sort_method=\"relevance\"):\n",
        "  handle = Entrez.esearch(db=\"gene\", term=query, retmax=count, retmode=\"xml\", sort=sort_method)\n",
        "  record = Entrez.read(handle)\n",
        "  return record['IdList']"
      ],
      "metadata": {
        "id": "UF_K4ZSE-2EW"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "id_list = request_gene_id(\"Hemoglobin\", 2)\n",
        "print(id_list)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "_VzQLXRfFIlW",
        "outputId": "e829c5aa-780b-422e-e20d-c5c167d2f1d0"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "['820216', '816103']\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def collate_ids(id_list):\n",
        "  ret = id_list[0]\n",
        "  for id in id_list[1:]:\n",
        "    ret += \",\"\n",
        "    ret += id\n",
        "  return ret"
      ],
      "metadata": {
        "id": "wvrMVlTdG_rn"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "id_string = collate_ids(id_list)\n",
        "print(id_string)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Fmby13mEHzds",
        "outputId": "f9ef0b17-99b2-433f-f551-a9bb14bf97d0"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "820216,816103\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def fetch_records(ids):\n",
        "  handle = Entrez.efetch(db=\"gene\", id=ids, retmode=\"xml\")\n",
        "  records = Entrez.read(handle)\n",
        "  return list(records)"
      ],
      "metadata": {
        "id": "lhZjLmsgFRWD"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "records = fetch_records(id_string)"
      ],
      "metadata": {
        "id": "buVFDgLVG9KC"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "def get_nuc_id_and_range(record):\n",
        "  seq_select = []\n",
        "  try:\n",
        "    seq_select = list(filter(lambda x: x[\"Gene-commentary_label\"]==\"RefSeqGene\", record['Entrezgene_locus']))[0]\n",
        "  except:\n",
        "    seq_select = record['Entrezgene_locus'][0]\n",
        "    print(f'Gene {record[\"Entrezgene_track-info\"][\"Gene-track\"][\"Gene-track_geneid\"]} does not have an independent RefSeq, defaulting to first entry')\n",
        "  try:\n",
        "    seq_interval = seq_select[\"Gene-commentary_seqs\"][0][\"Seq-loc_int\"][\"Seq-interval\"]\n",
        "    return (seq_interval[\"Seq-interval_id\"][\"Seq-id\"][\"Seq-id_gi\"], seq_interval[\"Seq-interval_from\"],  seq_interval[\"Seq-interval_to\"])\n",
        "  except:\n",
        "    print(\"Nucleotide sequence reference not found\")\n",
        "    return (\"SKIP\", \"SKIP\", \"SKIP\")"
      ],
      "metadata": {
        "id": "KCRVaC8HKHSS"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "info_list = [get_nuc_id_and_range(records[i]) for i in range(len(records))]\n",
        "print(info_list)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 418
        },
        "id": "U4duDf_qHmhe",
        "outputId": "bc8b67d8-2e62-483c-e456-c39f55795898"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "error",
          "ename": "KeyError",
          "evalue": "'Entrezgene_locus'",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-161-5ed5e647ecf0>\u001b[0m in \u001b[0;36mget_nuc_id_and_range\u001b[0;34m(record)\u001b[0m\n\u001b[1;32m      3\u001b[0m   \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m     \u001b[0mseq_select\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Gene-commentary_label\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m==\u001b[0m\u001b[0;34m\"RefSeqGene\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrecord\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Entrezgene_locus'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      5\u001b[0m   \u001b[0;32mexcept\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mKeyError\u001b[0m: 'Entrezgene_locus'",
            "\nDuring handling of the above exception, another exception occurred:\n",
            "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-175-dbf3917bd951>\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0minfo_list\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mget_nuc_id_and_range\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecords\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mi\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecords\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minfo_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m<ipython-input-175-dbf3917bd951>\u001b[0m in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0minfo_list\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mget_nuc_id_and_range\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecords\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mi\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecords\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minfo_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m<ipython-input-161-5ed5e647ecf0>\u001b[0m in \u001b[0;36mget_nuc_id_and_range\u001b[0;34m(record)\u001b[0m\n\u001b[1;32m      4\u001b[0m     \u001b[0mseq_select\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Gene-commentary_label\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m==\u001b[0m\u001b[0;34m\"RefSeqGene\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrecord\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Entrezgene_locus'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m   \u001b[0;32mexcept\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m     \u001b[0mseq_select\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrecord\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Entrezgene_locus'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      7\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mf'Gene {record[\"Entrezgene_track-info\"][\"Gene-track\"][\"Gene-track_geneid\"]} does not have an independent RefSeq, defaulting to first entry'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      8\u001b[0m   \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mKeyError\u001b[0m: 'Entrezgene_locus'"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def fetch_nucleotide_records(ids):\n",
        "  handle = Entrez.efetch(db=\"nuccore\", id=ids, rettype=\"fasta\", retmode=\"xml\")\n",
        "  records = Entrez.read(handle)\n",
        "  return list(records)"
      ],
      "metadata": {
        "id": "e5N_YsYrNPnK"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "id_list, start_list, end_list = zip(*info_list)\n",
        "records = fetch_nucleotide_records(collate_ids(id_list))"
      ],
      "metadata": {
        "id": "TKWlnyldN-VO"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "print(start_list)\n",
        "print(end_list)\n",
        "print(records[0][\"TSeq_sequence\"][int(start_list[0]):int(end_list[0])])"
      ],
      "metadata": {
        "id": "BwBFBq7gOEA_",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "639618bd-5b51-4bec-b608-767ea8fecb2f"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "('3276162', '6982530')\n",
            "('3277929', '6983776')\n",
            "GTTTTAGTGTACTGTTTTTTAAAAAAAGAAAAAATTGAACTAAAATAGATCCAAAATCTTGTGTCTGGAGAAGTAAAATTATTTGTAGAATGATTGTAAAATGATCCCCACGTTAACATCCATCTTGTGAAAATAAATACTTCAAACCATGATATTTCTCACGAATAACAATTTCAAGAAGAACTACAGTATCACGTATCTCCCTAATGATAGCACAAGATCCTTCTTTATAATTAAAATAGTGAACTGTAGAAAGTCAGAGAGCAACATAGTACACACACAGAAACACGTATATGTGTATCATGTATGTGGAATAGATTCATGTATGCGATACCCAAATGATCAATAGGGTTTTATGACTCTTCTTGTTTCATCTCGGTCTTGATGGCTAAAGCCAAGTGATCATAAGCTTGAGACCAAGCACCTTCCACTTCTTCATTGTATTTCTCCCCCAACCCCTCTTTCAATGTCCTTAGCAAAGCTTCTTTCACCACCTGCTTTCACATTCACACCTTATTAAAATGCGTTCAAATCGAAAATCAAAATCAGCCAAAATTAATGTGTATATATATTTTTTTTTAACATAACAGACCTCGAAGTGAGGGTCAATAACGCCGCTTTTGAGATGAATTGAGCCTAAATATTGGAGGGTTGTGTCAGCCACTACCACCTTTCCTTCCTCCCTCAGCTGTATAGCTGTTTCACATGTCTACACACAAACAAAATAAAATAAAAATTCATACATGTTATGCAAAGTCTTTTTCTTTTTTGTCTGTCTAAAACATGTTATGCAAAGTCTTAGAAGCCAAAAGTGAGTTGAACCAAACCAAGTCATAAACCCAAATTTAAAAAGTAAACGGAATTTGGTTTATATGGTTCTATTATAATAAGATTAGCAAAAAAGTAAAAATCCATAAAGCGACCCGAACCACTTGGATTCTTCAGTAACAATTCTTTATTGACAGAGAAATCTATGTTTGTTCTTAAAAATAAAATATCACAGAGTATTCTTTACTAGTATGAGATTTTTATTCTCAAAGAAGAAGACAAAGCCAACTAGCCAAGTTCAAACAAAATCGCAACTTGTGTGCACATGGCTGCGTCAATAAATGACAAGAAAAGTTAATTCAGACTACTATTTTCTATTATATATAAATGGTATATAATGAGTAAATAAAGATTCTTAGCTGTAAATAATGAAACATTCTACTTTCAATTTTAAGGAAGTGTAAGATAATGATACAGTATATGCAAGTGATTCACATATATGTAGATGTGGAAAATCGGAAAGTAAGTAATTACCATCTTGAAGACTTTAACAGCATGAGCTTTGAGTTTAGGATTGTTGTGAGGGACTTCATCTGAGTCTCTTAGGAAAGAGAACAAGCCTTTTGCTGCTGGTGCTATCTCCAGTATCCTATCACAATTATATTGTTCATTAGCTCGCATATATAAACAACATGTAAAGAGCTTATATATAACTAAGTATATATGGTTACTGTGAGAAGAAGTGAAGGCTGTATTTGGGGATGTCTTGTTTCAGTATCTCCCACGATTCCTTCACCAAAGCTTCTTGCTTCTCTGTAAACCCAATCTCTCCCATCTCTTTCTCTCTTTCTTTTTCTCTCACAGTTTGAAAAAAACACGAATATTTGTGTGTTTATATGTCTGTGTATCTATATATATATGGTATTCAATGGTCCTTTGGTTGGGTCTGTGAGCTACTTATGTAGAAGATTCTCTCAAATTTTATTTTATTTGACTAAA\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def get_seqs(info_list, gene_id_list):\n",
        "  ret = []\n",
        "  id_list, start_list, end_list = zip(*info_list)\n",
        "  fil_id_list = list(filter(lambda x: x != \"SKIP\", id_list))\n",
        "  records = fetch_nucleotide_records(collate_ids(fil_id_list))\n",
        "\n",
        "  offset = 0\n",
        "  for i in range(len(start_list)):\n",
        "    if id_list[i] == \"SKIP\":\n",
        "      ret.append((gene_id_list[i], \"NO SEQUENCE FOUND\"))\n",
        "      offset += 1\n",
        "      continue\n",
        "    start = int(start_list[i])\n",
        "    end = int(end_list[i])\n",
        "    ret.append((gene_id_list[i], records[i - offset][\"TSeq_sequence\"][start:end]))\n",
        "  return ret"
      ],
      "metadata": {
        "id": "Rno1pBP2HRPg"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "get_seqs(info_list)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "pLJKv2pQTbDl",
        "outputId": "f1ec9875-05bb-4ccc-e972-62a86ee8c8e3"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[('240255695',\n",
              "  'GTTTTAGTGTACTGTTTTTTAAAAAAAGAAAAAATTGAACTAAAATAGATCCAAAATCTTGTGTCTGGAGAAGTAAAATTATTTGTAGAATGATTGTAAAATGATCCCCACGTTAACATCCATCTTGTGAAAATAAATACTTCAAACCATGATATTTCTCACGAATAACAATTTCAAGAAGAACTACAGTATCACGTATCTCCCTAATGATAGCACAAGATCCTTCTTTATAATTAAAATAGTGAACTGTAGAAAGTCAGAGAGCAACATAGTACACACACAGAAACACGTATATGTGTATCATGTATGTGGAATAGATTCATGTATGCGATACCCAAATGATCAATAGGGTTTTATGACTCTTCTTGTTTCATCTCGGTCTTGATGGCTAAAGCCAAGTGATCATAAGCTTGAGACCAAGCACCTTCCACTTCTTCATTGTATTTCTCCCCCAACCCCTCTTTCAATGTCCTTAGCAAAGCTTCTTTCACCACCTGCTTTCACATTCACACCTTATTAAAATGCGTTCAAATCGAAAATCAAAATCAGCCAAAATTAATGTGTATATATATTTTTTTTTAACATAACAGACCTCGAAGTGAGGGTCAATAACGCCGCTTTTGAGATGAATTGAGCCTAAATATTGGAGGGTTGTGTCAGCCACTACCACCTTTCCTTCCTCCCTCAGCTGTATAGCTGTTTCACATGTCTACACACAAACAAAATAAAATAAAAATTCATACATGTTATGCAAAGTCTTTTTCTTTTTTGTCTGTCTAAAACATGTTATGCAAAGTCTTAGAAGCCAAAAGTGAGTTGAACCAAACCAAGTCATAAACCCAAATTTAAAAAGTAAACGGAATTTGGTTTATATGGTTCTATTATAATAAGATTAGCAAAAAAGTAAAAATCCATAAAGCGACCCGAACCACTTGGATTCTTCAGTAACAATTCTTTATTGACAGAGAAATCTATGTTTGTTCTTAAAAATAAAATATCACAGAGTATTCTTTACTAGTATGAGATTTTTATTCTCAAAGAAGAAGACAAAGCCAACTAGCCAAGTTCAAACAAAATCGCAACTTGTGTGCACATGGCTGCGTCAATAAATGACAAGAAAAGTTAATTCAGACTACTATTTTCTATTATATATAAATGGTATATAATGAGTAAATAAAGATTCTTAGCTGTAAATAATGAAACATTCTACTTTCAATTTTAAGGAAGTGTAAGATAATGATACAGTATATGCAAGTGATTCACATATATGTAGATGTGGAAAATCGGAAAGTAAGTAATTACCATCTTGAAGACTTTAACAGCATGAGCTTTGAGTTTAGGATTGTTGTGAGGGACTTCATCTGAGTCTCTTAGGAAAGAGAACAAGCCTTTTGCTGCTGGTGCTATCTCCAGTATCCTATCACAATTATATTGTTCATTAGCTCGCATATATAAACAACATGTAAAGAGCTTATATATAACTAAGTATATATGGTTACTGTGAGAAGAAGTGAAGGCTGTATTTGGGGATGTCTTGTTTCAGTATCTCCCACGATTCCTTCACCAAAGCTTCTTGCTTCTCTGTAAACCCAATCTCTCCCATCTCTTTCTCTCTTTCTTTTTCTCTCACAGTTTGAAAAAAACACGAATATTTGTGTGTTTATATGTCTGTGTATCTATATATATATGGTATTCAATGGTCCTTTGGTTGGGTCTGTGAGCTACTTATGTAGAAGATTCTCTCAAATTTTATTTTATTTGACTAAA'),\n",
              " ('240254678',\n",
              "  'AAGTAATTATATTTATTTTAAAGTCTATCAAAAATATCATAATCTTAATACAATTTGTAAGAAACATTTTTTTTTTGGGCAAAACAATTAGTAAGAAACTTGTATTCAAAATGATTAGGATTTTGGAATGCACACTATATATATATTATTGTCACTAAATCAAACCAAACCAAATAGAACAACAGTCATGAGAACAATTCAAAATGAAATATTTATTACAAGTTTACAACTATATAATAGTATATGATTTTTTAGTTGGAAAGATTCATTTCAGCTTTAATGGCAGCAACAAGGTGATCATAAGCCTGACCCCAAGCCACCTTCATCTCCGGTGACCACATCTCCGGCACTGCCTCCTTTATCGTCTCCAACAATGCATACTTGGCCACCTGCAGTTATAAATCATTTTTACATCAACCAAAAAAAATCAAGTTAACATATTTGTATGATAAAGAACATTTTGAGATATGACAAATAACTACTAACCTCAAAGTGTTCGTCAACGACACCGTATTTAGAATGGCTGGCTCCAAGTCTCTTCAAAGTAGTCTCCCTCACCGTAACTTTCCCTGTTTTCCTCAGTTGTACTGCTGATTCACAACACTGATAATAAACCCCAAAACTCAACAATCTTTGATTCGAATATATAAGCAAAATCATGTTATTTGATATTGATTATTACCATGACAAAAACAGACATTGCGTGAGGCTTGAGCTTTGGATTTTGCTCAGCAGGAATTGGTGAGTCTCTCAAGAAAGAGAACATCTTCTTCGTTGTTGGTGCAATCTCAAAGATCCTACAGTTCAAAATAGTAGTTCATATCTCAGACTATATACATAAAAAGAAAATAGAGAGAGATCAATGGGATCATTACTTACTTGATGAAGAGTTTGAGACCTAATTCAGCTGAGTTTTTCTTCATGACACTCCAAGACTTCACTACAAGAGCCTCTTGCTCTTCTGTGAACACAATCTTTCCTTCACTCTCCATAATATTTCACAACCTCTAAATGATTTAAAGTATACAACTCTCTGTTTTGTAGATCTTACTCCAATTATGAAAAGTATCCTATATATAGGTTTTGATAAAAGACCCTTTTGTGTTACCGAAGAGACAGTTCTTGATAAGCAAGTTTAAGATAAAGTTGCTTGGTTAAAAAGTGAAACCATGTGCTCTGTACTGGTAATGGAACATAGTTTGTAATGGTAGGCTTGACCAATTATTAGTCAAAACACTAAAGAAAA')]"
            ]
          },
          "metadata": {},
          "execution_count": 167
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def get_gene_names(record):\n",
        "  try:\n",
        "    return record[\"Entrezgene_gene\"][\"Gene-ref\"][\"Gene-ref_desc\"]\n",
        "  except:\n",
        "    print(f'Gene {record[\"Entrezgene_track-info\"][\"Gene-track\"][\"Gene-track_geneid\"]}: Gene Reference Description not found')"
      ],
      "metadata": {
        "id": "27BMCq4ZeVri"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [],
      "metadata": {
        "id": "R-VH-rIIfJrL"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "def get_sequence_from_query(query, count, fout=None):\n",
        "  gene_id_list = request_gene_id(query, count)\n",
        "  print(gene_id_list)\n",
        "  gene_records = fetch_records(collate_ids(gene_id_list))\n",
        "  info_list = [get_nuc_id_and_range(gene_records[i]) for i in range(len(gene_records))]\n",
        "  name_list = [get_gene_names(gene_records[i]) for i in range(len(gene_records))]\n",
        "  return list(zip(name_list, get_seqs(info_list, gene_id_list)))\n"
      ],
      "metadata": {
        "id": "BKgGzn6zTdqn"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "try:\n",
        "  print(get_sequence_from_query(\"Hemoglobin subunit beta\", 20))\n",
        "except Exception as error:\n",
        "  print(f\"Error Code: {error}\")"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "eYjAz0z-U1bW",
        "outputId": "ff92c6c1-1144-4b46-d6b1-d6c0d2e0b176"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "['3043', '24440', '3047', '3048', '3039', '3040', '3045', '396485', '3044', '100503605', '3046', '15129', '293267', '15130', '450978', '30216', '53335', '419079', '100134871', '476825']\n",
            "Gene 24440 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 396485 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 100503605 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 15129 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 293267 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 15130 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 450978 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 30216 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 419079 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 100134871 does not have an independent RefSeq, defaulting to first entry\n",
            "Gene 476825 does not have an independent RefSeq, defaulting to first entry\n",
            "Error Code: list index out of range\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "get_sequence_from_query(\"Hemoglobin subunit beta\", 3)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "4AogtXsSbMhE",
        "outputId": "a80d3c03-883e-4f13-ff7d-08f70dfa7bce"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "['3043', '24440', '3047']\n",
            "Gene 24440 does not have an independent RefSeq, defaulting to first entry\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[('hemoglobin subunit beta',\n",
              "  ('3043',\n",
              "   'ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTTGGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAGAGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTGCCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGGTGAGTCTATGGGACGCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATGTCATAGGAAGGGGATAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGCATCAGTGTGGAAGTCTCAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTTCTTTTGTTTAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGCCTTAACATTGTGTATAACAAAAGGAAATATCTCTGAGATACATTAAGTAACTTAAAAAAAAACTTTACACAGTCTGCCTAGTACATTACTATTTGGAATATATGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTATGGGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAATTTTGCATTTGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTCTAATACTTTCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTTTGCACCATTCTAAAGAATAACAGTGATAATTTCTGGGTTAAGGCAATAGCAATATCTCTGCATATAAATATTTCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTGCTAATAGCAGCTACAATCCAGCTACCATTCTGCTTTTATTTTATGGTTGGGATAAGGCTGGATTATTCTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTCATACCTCTTATCTTCCTCCCACAGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGCA')),\n",
              " ('hemoglobin subunit beta',\n",
              "  ('24440',\n",
              "   'GCAGTGAAAGTAAATGCCTTTAATTAGTAGGACAGATTTTCAAAGGTCTTTGTCATTTTGACAACAACTGACAGATGCTCTCTTGGGAACAATTGACCATTGCACAAAGACAAGAGCAGGAAAAGAGGTTTAGTGGTACTTGTGAGCCAGGGCACTGGCCACTCCAGCCACCACCTTCTGGAAGGCAGCCTGTGCACAGGGGGAGAATTCCTTGCCCAGGTGGTGGCCCAACACAATCACAATCATGTTGCCCAGGAGCTGTGGGAAGAGGGAAGAACCATCAACATAATTGCAGAGCAAAAATACCAGACACTTCAGGCTCATTTCAAATGGTGTTTTCGTTTCCAACTTAAAGTACTGAAAAATTATAATGAGAATTCTATGTCAGACAGAATTTATTGTAAAATATATTCTTCTCTTCCACTCTGGCATGAAAGCCAATTACTGCTACTACTCTTTAGAGCTGTGGGAAGAAACAGGGACTCACATATCTTCCTTGTCCTCAGAGCAAGTTACTAAGAAATATTTAAAAGAAAACAAAAAGTTGATTAAAAAAAGAGAAAATGGACTGAGGAGAAAAGAAAGAGGTAGGGTAATAGAAAGCAGAGAGAAGGACTGGGAAGAGAGGAAGAGGGGAAGCTGAGATCGGGATGGAAAGTAAATAAGTCAGTTAATTAATTTTTTTAAAAAGAAAAAACTGCATCTGAAAATTAAAAGTTTACCAAAGAAAGAGGAAATGACAACATAGAATAATAGAGTGAGAGGGAGAAGTGATTGTGAATAGAGGATAAAATAACTGGACTCCTGTCAACACTCCACAGGGCACATCCACACATCATCATCAAAACTGCTCCCTAGAGTGGCTTCCTCTTTCCTTCTGATAGGAATTTGAGCAGGAAAGCCACAGGAAGGACACCCAGTGAGGAGCCCATCAGACTCACCCTGAAGTTCTCAGGATCCACATGCAGCTTGTCACAGTGGAGTTCACTCAGATGAGCAAAGGTGCCCTTGAGGTTGTCCAAGTGTTTCAGGCCATCATTGAAGGCGTTTATCACCTTCTTGCCATGGGCCTTCACCTTAGGGTTACCCATGATAGCAGAGGCAGAGGACAGGTCCCCAAAGCTATCAAAGTACCTCTGGGTCCAAGGGTAGACAACCAGCAGCCTACAAAGGGAAACATAGCCAGGATACAATAAAAGTTAGTACCTGCTGGAAAGCAGACCTCTGTCTCCAAGCACCAAACTTCTACTTGCCTTGTAACCTGGATACCAACCTGCCCAGGGCCTCGCCACCAACATCATCAGGGTTCACCTTTCCCCACAGGCCATTAACAGCAGCCTTCTCAGCATCAGTCAGGTGCACCATGGTGTCTGTTTCTGAGTTTGTGAGTCAACACAACTATGTCAGAAGC')),\n",
              " ('hemoglobin subunit gamma 1',\n",
              "  ('3047',\n",
              "   'ACACTCGCTTCTGGAACGTCTGAGGTTATCAATAAGCTCCTAGTCCAGACGCCATGGGTCATTTCACAGAGGAGGACAAGGCTACTATCACAAGCCTGTGGGGCAAGGTGAATGTGGAAGATGCTGGAGGAGAAACCCTGGGAAGGTAGGCTCTGGTGACCAGGACAAGGGAGGGAAGGAAGGACCCTGTGCCTGGCAAAAGTCCAGGTCGCTTCTCAGGATTTGTGGCACCTTCTGACTGTCAAACTGTTCTTGTCAATCTCACAGGCTCCTGGTTGTCTACCCATGGACCCAGAGGTTCTTTGACAGCTTTGGCAACCTGTCCTCTGCCTCTGCCATCATGGGCAACCCCAAAGTCAAGGCACATGGCAAGAAGGTGCTGACTTCCTTGGGAGATGCCACAAAGCACCTGGATGATCTCAAGGGCACCTTTGCCCAGCTGAGTGAACTGCACTGTGACAAGCTGCATGTGGATCCTGAGAACTTCAAGGTGAGTCCAGGAGATGTTTCAGCCCTGTTGCCTTTAGTCTCGAGGCAACTTAGACAACGGAGTATTGATCTGAGCACAGCAGGGTGTGAGCTGTTTGAAGATACTGGGGTTGGGGGTGAAGAAACTGCAGAGGACTAACTGGGCTGAGACCCAGTGGTAATGTTTTAGGGCCTAAGGAGTGCCTCTAAAAATCTAGATGGACAATTTTGACTTTGAGAAAAGAGAGGTGGAAATGAGGAAAATGACTTTTCTTTATTAGATTCCAGTAGAAAGAACTTTCATCTTTCCCTCATTTTTGTTGTTTTAAAACATCTATCTGGAGGCAGGACAAGTATGGTCGTTAAAAAGATGCAGGCAGAAGGCATATATTGGCTCAGTCAAAGTGGGGAACTTTGGTGGCCAAACATACATTGCTAAGGCTATTCCTATATCAGCTGGACACATATAAAATGCTGCTAATGCTTCATTACAAACTTATATCCTTTAATTCCAGATGGGGGCAAAGTATGTCCAGGGGTGAGGAACAATTGAAACATTTGGGCTGGAGTAGATTTTGAAAGTCAGCTCTGTGTGTGTGTGTGTGTGTGCGCGCGCGCGTGTGTGTGTGTGTGTCAGCGTGTGTTTCTTTTAACGTCTTCAGCCTACAACATACAGGGTTCATGGTGGCAAGAAGATAGCAAGATTTAAATTATGGCCAGTGACTAGTGCTTGAAGGGGAACAACTACCTGCATTTAATGGGAAGGCAAAATCTCAGGCTTTGAGGGAAGTTAACATAGGCTTGATTCTGGGTGGAAGCTTGGTGTGTAGTTATCTGGAGGCCAGGCTGGAGCTCTCAGCTCACTATGGGTTCATCTTTATTGTCTCCTTTCATCTCAACAGCTCCTGGGAAATGTGCTGGTGACCGTTTTGGCAATCCATTTCGGCAAAGAATTCACCCCTGAGGTGCAGGCTTCCTGGCAGAAGATGGTGACTGCAGTGGCCAGTGCCCTGTCCTCCAGATACCACTGAGCTCACTGCCCATGATTCAGAGCTTTCAAGGATAGGCTTTATTCTGCAAGCAATACAAATAATAAATCTATTCTGCTGAGAGATCA'))]"
            ]
          },
          "metadata": {},
          "execution_count": 181
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "SInTbgEsU4Un"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}