New Mapping File.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# New Mapping File from NCBI Gene Dataset\n",
    "Downloaded: Jan 2, 2019"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import csv\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "file =  \"/Users/maayan/sigsets/Harmonizome/Data/All_Data.gene_info_010219\"\n",
    "mapping_file  = \"/Users/maayan/sigsets/Harmonizome/Data/mappingFileHMR_2019.tsv\"\n",
    "gene_sym_ids = \"/Users/maayan/sigsets/Harmonizome/Data/GeneSymbolsAndIDSHMR_2019.tsv\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Human, Mouse, and Rat only\n",
    "mapping_dict = {}\n",
    "with open(file) as o:\n",
    "    with open(gene_sym_ids, \"w\") as w:\n",
    "        with open(mapping_file, \"w\") as m:\n",
    "            csv_file = csv.reader(o, delimiter=\"\\t\")\n",
    "            w.write(\"Human, Mouse, and Rat Approved Symbol\tEntrez Gene ID(supplied by NCBI)\")\n",
    "            for row in csv_file:\n",
    "                tax_id = row[0]\n",
    "                if tax_id in [\"9606\", \"10090\", \"10116\"]:\n",
    "                    gene_id = row[1]\n",
    "                    if not row[2] == \"NEWENTRY\":\n",
    "                        sym = row[2]\n",
    "                    else: \n",
    "                        continue\n",
    "                    synonyms = [sym]\n",
    "                    if not row[4] == \"-\":\n",
    "                        synonyms = synonyms + row[4].split(\"|\")\n",
    "                else:\n",
    "                    continue\n",
    "                w.write(\"\\t\".join([tax_id, sym, gene_id]) + \"\\n\") # Add Taxon ID\n",
    "                if not tax_id in mapping_dict:\n",
    "                    mapping_dict[tax_id] = set([])\n",
    "                for syn in synonyms:\n",
    "                    if syn not in mapping_dict[tax_id]:\n",
    "                        mapping_dict[tax_id].add(syn)\n",
    "                        m.write(\"\\t\".join([tax_id, syn, sym])+ \"\\n\")\n",
    "                        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "getGeneIDsHMR_updated = pd.read_csv('/Users/maayan/sigsets/Harmonizome/Data/GeneSymbolsAndIDSHMR_2019.tsv', sep='\\t', index_col=[0,1]).sort_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(9606,\"A2MP1\") in getGeneIDsHMR_updated.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "mappingDFHMR_updated = pd.read_csv('/Users/maayan/sigsets/Harmonizome/Data/mappingFileHMR_2019.tsv', sep='\\t', header=None, index_col=[0,1]).sort_index()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(9606,\"(FM-3)\") in mappingDFHMR_updated.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "                               2\n",
       "0     1                         \n",
       "9606  (FM-3)               NMUR1\n",
       "      (IV)-44        IGHVIV-44-1\n",
       "      (ppGpp)ase           HDDC3\n",
       "      0610011B16Rik        CORO7\n",
       "      0610037N12Rik         POP7\n",
       "      0710008D09Rik       UQCR11\n",
       "      0808y08y          NFYC-AS1\n",
       "      1-12P             IGHV1-12\n",
       "      1-14P             IGHV1-14\n",
       "      1-17P             IGHV1-17\n",
       "      1-67P             IGHV1-67\n",
       "      1-68P             IGHV1-68\n",
       "      1-8D                IFITM2\n",
       "      1-8U                IFITM3\n",
       "      1-AGPAT 6            GPAT4\n",
       "      1-AGPAT1            AGPAT1\n",
       "      1-AGPAT2            AGPAT2\n",
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       "      1-Cys                PRDX6\n",
       "      1/2-SBSRNA4     SEC24B-AS1\n",
       "      10-FTHFDH          ALDH1L1\n",
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       "      101F10.1             KNOP1\n",
       "      101F6             CYB561D2\n",
       "      104p               TUBGCP3\n",
       "      105A              SNORA73B\n",
       "      105B               RNU105B\n",
       "      10C                ARHGAP9\n",
       "      10q23del            BMPR1A\n",
       "      11-DH              HSD11B1\n",
       "...                          ...\n",
       "10116 tpcr07             Olr1398\n",
       "      tpcr09              Olr737\n",
       "      tpcr10             Olr1404\n",
       "      tpcr13             Olr1366\n",
       "      tpcr18             Olr1307\n",
       "      tpcr19             Olr1226\n",
       "      tpcr21             Olr1283\n",
       "      tpcr38             Olr1606\n",
       "      trk-B                Ntrk2\n",
       "      trkB                 Ntrk2\n",
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       "      try1                Prss58\n",
       "      uKATP-1              Kcnj8\n",
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       "      uPAR-2               Plaur\n",
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       "      ufd2a                Ube4b\n",
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       "      vip/phi27              Vip\n",
       "      vms-tm2             Cd99l2\n",
       "      wbp-11               Wbp11\n",
       "      x85                  Dus1l\n",
       "      xylt-II              Xylt2\n",
       "      y+LAT1              Slc7a7\n",
       "      zbs559            Map1lc3b\n",
       "      zgc:101121          Zfand6\n",
       "      zgc:66482          Pik3ip1\n",
       "      zif-268               Egr1\n",
       "      NaN                 Scn11a\n",
       "\n",
       "[329092 rows x 1 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mappingDFHMR_updated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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