Untitled.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "d9452e86",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-18T16:11:11.545628Z",
     "start_time": "2023-01-18T16:11:11.435483Z"
    }
   },
   "outputs": [],
   "source": [
    "import biorosetta as m\n",
    "import importlib as imp\n",
    "imp.reload(m)\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "fb6a7bb7",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-18T16:11:11.665818Z",
     "start_time": "2023-01-18T16:11:11.635389Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/m7/zm8cz6t57dx2yksvbbs0zlh40000gp/T/ipykernel_62901/3320118968.py:1: DeprecationWarning: Importing display from IPython.core.display is deprecated since IPython 7.14, please import from IPython display\n",
      "  from IPython.core.display import display, HTML\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<style>.container { width:50% !important; }</style>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from IPython.core.display import display, HTML\n",
    "display(HTML(\"<style>.container { width:50% !important; }</style>\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c9619b0f",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "d835e49f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-18T16:11:14.078027Z",
     "start_time": "2023-01-18T16:11:12.811957Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['MT-TF', '5S_rRNA', 'N/A', 'XKRY2']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import biorosetta as br\n",
    "\n",
    "genes_to_convert = ['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646']\n",
    "\n",
    "idm = br.EnsemblBiomartMapper()\n",
    "idm.convert(genes_to_convert,'ensg','symb',multi_hits='all',df=False).tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "0b33ab2f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-17T18:26:08.856148Z",
     "start_time": "2023-01-17T18:25:56.988968Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "- Biomart data has not been downloaded yet.\n",
      "- Downloading up-to-date gene annotation data from Ensembl Biomart (http://www.ensembl.org/biomart) to /Users/reema/Postdoc/Libs/biorosetta/data/ensembl.tsv.\n",
      "- This operation has to be performed only once and it lasts less than a minute.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/reema/Postdoc/Libs/biorosetta/data/ensembl.tsv: 3.43MiB [00:09, 382kiB/s]\n"
     ]
    }
   ],
   "source": [
    "import biorosetta as br\n",
    "idm = br.EnsemblBiomartMapper()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "99155ad7",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-17T18:50:19.717402Z",
     "start_time": "2023-01-17T18:50:17.100352Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-4...done.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "['MT-TF', '5S_rRNA', 'TTTY15', 'XKRY2']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import biorosetta as br\n",
    "\n",
    "genes_to_convert = ['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646']\n",
    "\n",
    "idm = br.CompoundMapper([br.EnsemblBiomartMapper(),br.HGNCBiomartMapper(),br.MyGeneMapper()])\n",
    "idm.convert(genes_to_convert,'ensg','symb',multi_hits='consensus',df=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "b76ba809",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-17T18:50:40.213265Z",
     "start_time": "2023-01-17T18:50:38.855608Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-4...done.\n"
     ]
    },
    {
     "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>ensembl</th>\n",
       "      <th>hgnc</th>\n",
       "      <th>mygene</th>\n",
       "      <th>output</th>\n",
       "      <th>Mismatch</th>\n",
       "      <th>ensembl_hits</th>\n",
       "      <th>hgnc_hits</th>\n",
       "      <th>mygene_hits</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MT-TF</td>\n",
       "      <td>MT-TF</td>\n",
       "      <td>TRNF</td>\n",
       "      <td>MT-TF</td>\n",
       "      <td>True</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>5S_rRNA</td>\n",
       "      <td>N/A</td>\n",
       "      <td>5S_rRNA</td>\n",
       "      <td>5S_rRNA</td>\n",
       "      <td>False</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>N/A</td>\n",
       "      <td>TTTY15</td>\n",
       "      <td>N/A</td>\n",
       "      <td>TTTY15</td>\n",
       "      <td>False</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>XKRY2</td>\n",
       "      <td>XKRYP7</td>\n",
       "      <td>XKRY2</td>\n",
       "      <td>XKRY2</td>\n",
       "      <td>True</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   ensembl    hgnc   mygene   output  Mismatch  ensembl_hits  hgnc_hits  \\\n",
       "0    MT-TF   MT-TF     TRNF    MT-TF      True           1.0        1.0   \n",
       "1  5S_rRNA     N/A  5S_rRNA  5S_rRNA     False           1.0        0.0   \n",
       "2      N/A  TTTY15      N/A   TTTY15     False           0.0        1.0   \n",
       "3    XKRY2  XKRYP7    XKRY2    XKRY2      True           1.0        1.0   \n",
       "\n",
       "   mygene_hits  \n",
       "0          1.0  \n",
       "1          1.0  \n",
       "2          0.0  \n",
       "3          1.0  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idm.convert(genes_to_convert,'ensg','symb',multi_hits='consensus',df=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f3f1b163",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1c8f27f5",
   "metadata": {
    "ExecuteTime": {
     "start_time": "2023-01-17T18:41:39.756Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> \u001b[0;32m/Users/reema/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/generic.py\u001b[0m(5902)\u001b[0;36m__getattr__\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m   5900 \u001b[0;31m        ):\n",
      "\u001b[0m\u001b[0;32m   5901 \u001b[0;31m            \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m-> 5902 \u001b[0;31m        \u001b[0;32mreturn\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattribute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   5903 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   5904 \u001b[0;31m    \u001b[0;32mdef\u001b[0m \u001b[0m__setattr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> u\n",
      "> \u001b[0;32m/Users/reema/Postdoc/Libs/biorosetta/classes.py\u001b[0m(211)\u001b[0;36mconvert\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m    209 \u001b[0;31m                                \u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Mismatch'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\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[0mx\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_fill_value\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnunique\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    210 \u001b[0;31m                        \u001b[0;32mfor\u001b[0m \u001b[0msrc_id\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msrc_ids\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m--> 211 \u001b[0;31m                                \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msrc_id\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0;34m'N/A'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34mf'{src_id}_hits'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msrc_id\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'|'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\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[0;32m    212 \u001b[0;31m                                \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msrc_id\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'N/A'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34mf'{src_id}_hits'\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[0m\n",
      "\u001b[0m\u001b[0;32m    213 \u001b[0;31m                        \u001b[0;32mreturn\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> out_df\n",
      "   ensembl    hgnc   mygene   output Mismatch\n",
      "0    MT-TF   MT-TF     TRNF    MT-TF     True\n",
      "1  5S_rRNA     N/A  5S_rRNA  5S_rRNA    False\n",
      "2      N/A  TTTY15      N/A   TTTY15    False\n",
      "3    XKRY2  XKRYP7    XKRY2    XKRY2     True\n",
      "ipdb> type(out_df)\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "ipdb> out_df.columns\n",
      "MultiIndex([( 'ensembl',),\n",
      "            (    'hgnc',),\n",
      "            (  'mygene',),\n",
      "            (  'output',),\n",
      "            ('Mismatch',)],\n",
      "           )\n",
      "ipdb> exit\n"
     ]
    }
   ],
   "source": [
    "%debug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "789725b5",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-17T16:39:23.369417Z",
     "start_time": "2023-01-17T16:39:22.009301Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-4...done.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/reema/Postdoc/Libs/biorosetta/classes.py:223: FutureWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)`\n",
      "  report_df.loc[report_df[src_id]!='N/A',f'{src_id}_hits'] = report_df[src_id].str.split('|').apply(lambda x: len(x))\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ensembl</th>\n",
       "      <th>hgnc</th>\n",
       "      <th>mygene</th>\n",
       "      <th>Mismatch</th>\n",
       "      <th>ensembl_hits</th>\n",
       "      <th>hgnc_hits</th>\n",
       "      <th>mygene_hits</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MT-TF</td>\n",
       "      <td>MT-TF</td>\n",
       "      <td>TRNF</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>5S_rRNA</td>\n",
       "      <td>N/A</td>\n",
       "      <td>5S_rRNA</td>\n",
       "      <td>False</td>\n",
       "      <td>1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TTTY15</td>\n",
       "      <td>TTTY15</td>\n",
       "      <td>N/A</td>\n",
       "      <td>False</td>\n",
       "      <td>1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>XKRY2</td>\n",
       "      <td>XKRYP7</td>\n",
       "      <td>XKRY2</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   ensembl    hgnc   mygene  Mismatch  ensembl_hits  hgnc_hits  mygene_hits\n",
       "0    MT-TF   MT-TF     TRNF      True             1        1.0          1.0\n",
       "1  5S_rRNA     N/A  5S_rRNA     False             1        0.0          1.0\n",
       "2   TTTY15  TTTY15      N/A     False             1        1.0          0.0\n",
       "3    XKRY2  XKRYP7    XKRY2      True             1        1.0          1.0"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idm.convert(['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646'],'ensg','symb',multi_hits='all',df=True)[1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "8893d8ae",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-17T16:37:52.131487Z",
     "start_time": "2023-01-17T16:25:39.658795Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> \u001b[0;32m/Users/reema/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/generic.py\u001b[0m(5902)\u001b[0;36m__getattr__\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m   5900 \u001b[0;31m        ):\n",
      "\u001b[0m\u001b[0;32m   5901 \u001b[0;31m            \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m-> 5902 \u001b[0;31m        \u001b[0;32mreturn\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattribute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   5903 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   5904 \u001b[0;31m    \u001b[0;32mdef\u001b[0m \u001b[0m__setattr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> u\n",
      "> \u001b[0;32m/Users/reema/Postdoc/Libs/biorosetta/classes.py\u001b[0m(35)\u001b[0;36mfilter_multi_hits\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m     33 \u001b[0;31m        \u001b[0;32mdef\u001b[0m \u001b[0mfilter_multi_hits\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmulti_hits\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[0;32m     34 \u001b[0;31m                \u001b[0;32mif\u001b[0m \u001b[0mmulti_hits\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'first'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m---> 35 \u001b[0;31m                        \u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontains\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[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontains\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[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'|'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstr\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[0;32m     36 \u001b[0;31m                \u001b[0;32mif\u001b[0m \u001b[0mmulti_hits\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'shortest'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m     37 \u001b[0;31m                        \u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontains\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[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontains\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[0mstr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'|'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mmin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlen\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\n",
      "ipdb> out_df\n",
      "             query   symbol\n",
      "0  ENSG00000210049     TRNF\n",
      "1  ENSG00000278457  5S_rRNA\n",
      "2  ENSG00000233864      N/A\n",
      "3  ENSG00000244646    XKRY2\n",
      "ipdb> out_df['symbol']\n",
      "0       TRNF\n",
      "1    5S_rRNA\n",
      "2        N/A\n",
      "3      XKRY2\n",
      "Name: symbol, dtype: object\n",
      "ipdb> u\n",
      "> \u001b[0;32m/Users/reema/Postdoc/Libs/biorosetta/classes.py\u001b[0m(174)\u001b[0;36mconvert\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m    172 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    173 \u001b[0;31m                \u001b[0mout_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mid_relabel\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mid_out\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfillna\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_fill_value\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreset_index\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[0;32m--> 174 \u001b[0;31m                \u001b[0mout_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfilter_multi_hits\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmulti_hits\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    175 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    176 \u001b[0;31m                \u001b[0mout_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreindex\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mid_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> l\n",
      "\u001b[1;32m    169 \u001b[0m                \u001b[0mid_relabel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m'entr'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'entrezgene'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'symb'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'symbol'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'ensg'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'ensembl.gene'\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m    170 \u001b[0m\t\toutput = MyGeneMapper.mg.getgenes(id_list, scopes=id_relabel[id_in], fields=id_relabel[id_out],\n",
      "\u001b[1;32m    171 \u001b[0m\t\t\t\t\t\t\t\t\tspecies='human', as_dataframe=True, returnall=False)\n",
      "\u001b[1;32m    172 \u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m    173 \u001b[0m                \u001b[0mout_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mid_relabel\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mid_out\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfillna\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_fill_value\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreset_index\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[0;32m--> 174 \u001b[0;31m                \u001b[0mout_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfilter_multi_hits\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmulti_hits\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    175 \u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m    176 \u001b[0m                \u001b[0mout_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreindex\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mid_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m    177 \u001b[0m                \u001b[0;32mif\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m    178 \u001b[0m                        \u001b[0;32mreturn\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m    179 \u001b[0m                \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\n",
      "ipdb> out_df\n",
      "             query   symbol\n",
      "0  ENSG00000210049     TRNF\n",
      "1  ENSG00000278457  5S_rRNA\n",
      "2  ENSG00000233864      N/A\n",
      "3  ENSG00000244646    XKRY2\n",
      "ipdb> output\n",
      "                             _id  _version   symbol notfound\n",
      "query                                                       \n",
      "ENSG00000210049             4558       1.0     TRNF      NaN\n",
      "ENSG00000278457  ENSG00000278457       1.0  5S_rRNA      NaN\n",
      "ENSG00000233864              NaN       NaN      NaN     True\n",
      "ENSG00000244646  ENSG00000244646       1.0    XKRY2      NaN\n",
      "ipdb> output[id_relabel[id_out]]\n",
      "query\n",
      "ENSG00000210049       TRNF\n",
      "ENSG00000278457    5S_rRNA\n",
      "ENSG00000233864        NaN\n",
      "ENSG00000244646      XKRY2\n",
      "Name: symbol, dtype: object\n",
      "ipdb> output[id_relabel[id_out]].fillna(self._fill_value).reset_index()\n",
      "             query   symbol\n",
      "0  ENSG00000210049     TRNF\n",
      "1  ENSG00000278457  5S_rRNA\n",
      "2  ENSG00000233864      N/A\n",
      "3  ENSG00000244646    XKRY2\n",
      "ipdb> output[id_relabel[id_out]].fillna(self._fill_value)\n",
      "query\n",
      "ENSG00000210049       TRNF\n",
      "ENSG00000278457    5S_rRNA\n",
      "ENSG00000233864        N/A\n",
      "ENSG00000244646      XKRY2\n",
      "Name: symbol, dtype: object\n",
      "ipdb> type(output[id_relabel[id_out]].fillna(self._fill_value).reset_index())\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "ipdb> type(output[id_relabel[id_out]].fillna(self._fill_value).reset_index(drop=True))\n",
      "<class 'pandas.core.series.Series'>\n",
      "ipdb> output[id_relabel[id_out]].fillna(self._fill_value).reset_index(drop=True)\n",
      "0       TRNF\n",
      "1    5S_rRNA\n",
      "2        N/A\n",
      "3      XKRY2\n",
      "Name: symbol, dtype: object\n",
      "ipdb> output[id_relabel[id_out]].fillna(self._fill_value)\n",
      "query\n",
      "ENSG00000210049       TRNF\n",
      "ENSG00000278457    5S_rRNA\n",
      "ENSG00000233864        N/A\n",
      "ENSG00000244646      XKRY2\n",
      "Name: symbol, dtype: object\n",
      "ipdb> exit\n"
     ]
    }
   ],
   "source": [
    "%debug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "2e686ab8",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-01-17T16:24:05.433528Z",
     "start_time": "2023-01-17T16:24:03.925791Z"
    },
    "scrolled": false
   },
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "module 'biorosetta' has no attribute 'IDMapper'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[7], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m sources \u001b[38;5;241m=\u001b[39m [m\u001b[38;5;241m.\u001b[39mEnsemblMapper(),m\u001b[38;5;241m.\u001b[39mHGNCMapper()]\n\u001b[1;32m      2\u001b[0m \u001b[38;5;66;03m#sources2 = [m.HGNCBiomart(),m.EnsemblBiomart()]\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m idm \u001b[38;5;241m=\u001b[39m \u001b[43mm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mIDMapper\u001b[49m(sources)\n\u001b[1;32m      4\u001b[0m \u001b[38;5;66;03m#idm2 = m.IDMapper(sources2)\u001b[39;00m\n",
      "\u001b[0;31mAttributeError\u001b[0m: module 'biorosetta' has no attribute 'IDMapper'"
     ]
    }
   ],
   "source": [
    "sources = [m.EnsemblMapper(),m.HGNCMapper()]\n",
    "#sources2 = [m.HGNCBiomart(),m.EnsemblBiomart()]\n",
    "idm = m.IDMapper(sources)\n",
    "#idm2 = m.IDMapper(sources2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "00a9f533",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:02:14.566122Z",
     "start_time": "2022-12-28T23:02:14.544090Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(['ENSG00000268895'],\n",
       "                   ensembl             hgnc Mismatch\n",
       " FLJ23569  ENSG00000268895  ENSG00000268895    False)"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idm.convert('FLJ23569','symb','ensg', report=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "234be241",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(idm.convert(['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646'],'ensg','symb',report=True)[0])\n",
    "print(idm2.convert(['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646'],'ensg','symb'))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7fd7aaf2",
   "metadata": {},
   "source": [
    "# MyGene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "80e32f1a",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T16:06:42.076892Z",
     "start_time": "2022-12-29T16:06:39.824883Z"
    }
   },
   "outputs": [],
   "source": [
    "idm = m.IDMapper([m.EnsemblBiomart(list_all_hits=True),m.HGNCBiomart(list_all_hits=True),m.MyGene()])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "21798c27",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T16:17:01.497930Z",
     "start_time": "2022-12-29T16:16:52.234083Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-1000...done.\n",
      "querying 1001-2000...done.\n",
      "querying 2001-3000...done.\n"
     ]
    }
   ],
   "source": [
    "res,report = idm.convert(idm._sources[0]._lookup['ensg']['entr'].index[2000:5000], 'ensg', 'entr',report=True)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "4ad55c3b",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T16:12:29.997412Z",
     "start_time": "2022-12-29T16:12:29.984857Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr>\n",
       "      <th></th>\n",
       "      <th>ensembl</th>\n",
       "      <th>hgnc</th>\n",
       "      <th>mygene</th>\n",
       "      <th>Mismatch</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ensg</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000198888</th>\n",
       "      <td>4535</td>\n",
       "      <td>4535</td>\n",
       "      <td>4535</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000198763</th>\n",
       "      <td>4536</td>\n",
       "      <td>4536</td>\n",
       "      <td>4536</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000198804</th>\n",
       "      <td>4512</td>\n",
       "      <td>4512</td>\n",
       "      <td>4512</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000210151</th>\n",
       "      <td>113219467</td>\n",
       "      <td>4574</td>\n",
       "      <td>113219467</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000198712</th>\n",
       "      <td>4513</td>\n",
       "      <td>4513</td>\n",
       "      <td>4513</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000226634</th>\n",
       "      <td>23564</td>\n",
       "      <td>N/A</td>\n",
       "      <td>23564</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000277614</th>\n",
       "      <td>6447</td>\n",
       "      <td>N/A</td>\n",
       "      <td>6447</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000235941</th>\n",
       "      <td>3303</td>\n",
       "      <td>N/A</td>\n",
       "      <td>3303</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000277086</th>\n",
       "      <td>54893</td>\n",
       "      <td>N/A</td>\n",
       "      <td>54893</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000240389</th>\n",
       "      <td>80864</td>\n",
       "      <td>N/A</td>\n",
       "      <td>80864</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1000 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   ensembl  hgnc     mygene Mismatch\n",
       "ensg                                                \n",
       "ENSG00000198888       4535  4535       4535    False\n",
       "ENSG00000198763       4536  4536       4536    False\n",
       "ENSG00000198804       4512  4512       4512    False\n",
       "ENSG00000210151  113219467  4574  113219467     True\n",
       "ENSG00000198712       4513  4513       4513    False\n",
       "...                    ...   ...        ...      ...\n",
       "ENSG00000226634      23564   N/A      23564    False\n",
       "ENSG00000277614       6447   N/A       6447    False\n",
       "ENSG00000235941       3303   N/A       3303    False\n",
       "ENSG00000277086      54893   N/A      54893    False\n",
       "ENSG00000240389      80864   N/A      80864    False\n",
       "\n",
       "[1000 rows x 4 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "report"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "15f0af99",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T16:17:02.129646Z",
     "start_time": "2022-12-29T16:17:02.116226Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
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       "\n",
       "    .dataframe thead tr th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe thead tr:last-of-type th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr>\n",
       "      <th></th>\n",
       "      <th>ensembl</th>\n",
       "      <th>hgnc</th>\n",
       "      <th>mygene</th>\n",
       "      <th>Mismatch</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ensg</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000207476</th>\n",
       "      <td>124905313</td>\n",
       "      <td>106480567</td>\n",
       "      <td>124905313</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000258636</th>\n",
       "      <td>124907392</td>\n",
       "      <td>105370469</td>\n",
       "      <td>124907392</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000228636</th>\n",
       "      <td>124902542</td>\n",
       "      <td>105376402</td>\n",
       "      <td>124902542</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000280263</th>\n",
       "      <td>440888</td>\n",
       "      <td>644773</td>\n",
       "      <td>440888</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000233780</th>\n",
       "      <td>101930748</td>\n",
       "      <td>440125</td>\n",
       "      <td>101930748</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000253505</th>\n",
       "      <td>124901880</td>\n",
       "      <td>123466202</td>\n",
       "      <td>124901880</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   ensembl       hgnc     mygene Mismatch\n",
       "ensg                                                     \n",
       "ENSG00000207476  124905313  106480567  124905313     True\n",
       "ENSG00000258636  124907392  105370469  124907392     True\n",
       "ENSG00000228636  124902542  105376402  124902542     True\n",
       "ENSG00000280263     440888     644773     440888     True\n",
       "ENSG00000233780  101930748     440125  101930748     True\n",
       "ENSG00000253505  124901880  123466202  124901880     True"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "report[report.Mismatch.squeeze()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 200,
   "id": "e04dad72",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T15:41:28.542022Z",
     "start_time": "2022-12-29T15:37:34.294917Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> \u001b[0;32m/Users/reema/Postdoc/Libs/biorosetta/main.py\u001b[0m(181)\u001b[0;36m<lambda>\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m    179 \u001b[0;31m                        \u001b[0mreport_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconcat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msrc_id\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0msrc_id\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msrc_ids\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    180 \u001b[0;31m                        \u001b[0;32mif\u001b[0m \u001b[0many\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msrc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_list_all_hits\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0msrc\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_sources\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[0;32m--> 181 \u001b[0;31m                                \u001b[0mreport_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Mismatch'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreport_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mset\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mintersection\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0melem\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'|'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0melem\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mx\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_fill_value\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[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    182 \u001b[0;31m                        \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m    183 \u001b[0;31m                                \u001b[0mreport_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Mismatch'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreport_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\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[0mx\u001b[0m\u001b[0;34m!=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_fill_value\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnunique\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> [set(elem.split('|')) for elem in x[x != self._fill_value]]\n",
      "[]\n",
      "ipdb> exit\n"
     ]
    }
   ],
   "source": [
    "%debug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 186,
   "id": "04c0ad33",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T15:25:02.421128Z",
     "start_time": "2022-12-29T15:25:00.958491Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-5...done.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "['4558', 'N/A', '64595', '353515', '1673|100289462|124906748']"
      ]
     },
     "execution_count": 186,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idm.convert(['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646','ENSG00000285181'],'ensg','entr',report=True)[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 184,
   "id": "d6fe2907",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T15:24:42.406086Z",
     "start_time": "2022-12-29T15:24:42.401096Z"
    }
   },
   "outputs": [],
   "source": [
    "tempvar = idm._sources[0]._lookup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 185,
   "id": "99b60684",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T15:24:46.714918Z",
     "start_time": "2022-12-29T15:24:46.695578Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'ensg': {'entr': ensg\n",
       "  ENSG00000198888                                                 4535\n",
       "  ENSG00000198763                                                 4536\n",
       "  ENSG00000198804                                                 4512\n",
       "  ENSG00000210151                                            113219467\n",
       "  ENSG00000198712                                                 4513\n",
       "  ENSG00000228253                                                 4509\n",
       "  ENSG00000198899                                                 4508\n",
       "  ENSG00000198938                                                 4514\n",
       "  ENSG00000198840                                                 4537\n",
       "  ENSG00000212907                                                 4539\n",
       "  ENSG00000198886                                                 4538\n",
       "  ENSG00000198786                                                 4540\n",
       "  ENSG00000198695                                                 4541\n",
       "  ENSG00000198727                                                 4519\n",
       "  ENSG00000271254                                            102724250\n",
       "  ENSG00000280663                                                55251\n",
       "  ENSG00000262826                                                65123\n",
       "  ENSG00000273947                                                 3804\n",
       "  ENSG00000273735                                                 3812\n",
       "  ENSG00000275717                                                 3811\n",
       "  ENSG00000276379                                                 3811\n",
       "  ENSG00000276433                                               115653\n",
       "  ENSG00000275442                                                79166\n",
       "  ENSG00000274692                                                 3802\n",
       "  ENSG00000277484                                                 3804\n",
       "  ENSG00000275062                                               115653\n",
       "  ENSG00000277554                                                 3804\n",
       "  ENSG00000277272                                                 3811\n",
       "  ENSG00000277044                                                 4987\n",
       "  ENSG00000277339                                                 2832\n",
       "  ENSG00000274807                                                 3809\n",
       "  ENSG00000274714                                                 3809\n",
       "  ENSG00000276876                                                 4661\n",
       "  ENSG00000277334                                                 9437\n",
       "  ENSG00000276885                                                 3809\n",
       "  ENSG00000275786                                                 3811\n",
       "  ENSG00000277982                                                 3812\n",
       "  ENSG00000277267                                                79166\n",
       "  ENSG00000273510                                                 3802\n",
       "  ENSG00000274324                                                 3809\n",
       "  ENSG00000276423                                                 3811\n",
       "  ENSG00000276534                                                 3813\n",
       "  ENSG00000276820                                                 3802\n",
       "  ENSG00000278731                                                 3803\n",
       "  ENSG00000278306                                                 3808\n",
       "  ENSG00000277620                                               115653\n",
       "  ENSG00000281362                                               339822\n",
       "  ENSG00000274948                                                 3811\n",
       "  ENSG00000276858                                                 2204\n",
       "  ENSG00000276328                                               115653\n",
       "                                           ...                        \n",
       "  ENSG00000285181                             1673|100289462|124906748\n",
       "  ENSG00000285285    100169753|124905422|124905424|124905425|124905...\n",
       "  ENSG00000285286                                  100131980|124900627\n",
       "  ENSG00000285356                                     503618|124906746\n",
       "  ENSG00000285376                                     414325|124906744\n",
       "  ENSG00000285411                                     504180|124906747\n",
       "  ENSG00000285432                              245910|503614|124906743\n",
       "  ENSG00000285433                             1673|100289462|124906748\n",
       "  ENSG00000285479                                        775|100874369\n",
       "  ENSG00000285607    441327|645651|124906721|124906722|124906751|12...\n",
       "  ENSG00000285617                                     245909|124906749\n",
       "  ENSG00000285765                                     645572|124906757\n",
       "  ENSG00000285795                                     645572|124906757\n",
       "  ENSG00000285832                                        441317|441327\n",
       "  ENSG00000285950                           441328|124906735|124906766\n",
       "  ENSG00000285962    441327|645651|124906721|124906722|124906751|12...\n",
       "  ENSG00000285975                                        441317|441327\n",
       "  ENSG00000286014                           641776|105180390|105180391\n",
       "  ENSG00000286038                           641776|105180390|105180391\n",
       "  ENSG00000286137                           641776|105180390|105180391\n",
       "  ENSG00000286190                                     728392|124900388\n",
       "  ENSG00000287664    102723851|102724956|105371848|105371853|124900636\n",
       "  ENSG00000288147                                     389831|124900580\n",
       "  ENSG00000288164                                  102723573|102724737\n",
       "  ENSG00000288184                                  124907096|124907358\n",
       "  ENSG00000288205                        124904108|124904706|124906683\n",
       "  ENSG00000288214                 283767|124900581|124905482|124907501\n",
       "  ENSG00000288249                                  124907096|124907358\n",
       "  ENSG00000288273                                        255313|728062\n",
       "  ENSG00000288309                                      10407|124906741\n",
       "  ENSG00000288326    106632260|124900510|124907114|124907115|124907...\n",
       "  ENSG00000288357                                           3810|57292\n",
       "  ENSG00000288387    109910381|124900510|124907114|124907115|124907...\n",
       "  ENSG00000288487                                          3808|553128\n",
       "  ENSG00000288811              105372935|105372942|105377182|105379548\n",
       "  ENSG00000288905                                     645166|107985200\n",
       "  ENSG00000289007                                  101928092|124908546\n",
       "  ENSG00000290355                                     727856|100287029\n",
       "  ENSG00000290614                                        150527|646743\n",
       "  ENSG00000290633                           727856|100287596|100288486\n",
       "  ENSG00000290751                                          6953|401285\n",
       "  ENSG00000290824                           727856|100287596|100288486\n",
       "  ENSG00000290825           84771|727856|100287102|100287596|102725121\n",
       "  ENSG00000291016                                         84559|401634\n",
       "  ENSG00000291031                                     286554|105377223\n",
       "  ENSG00000291050                                  100132288|100233156\n",
       "  ENSG00000291150                                     645166|107985911\n",
       "  ENSG00000291153                                      64940|101929736\n",
       "  ENSG00000291154                                            5380|5382\n",
       "  ENSG00000291158                                         57234|388692\n",
       "  Length: 29912, dtype: object,\n",
       "  'symb': ensg\n",
       "  ENSG00000210049           MT-TF\n",
       "  ENSG00000211459         MT-RNR1\n",
       "  ENSG00000210077           MT-TV\n",
       "  ENSG00000210082         MT-RNR2\n",
       "  ENSG00000209082          MT-TL1\n",
       "  ENSG00000198888          MT-ND1\n",
       "  ENSG00000210100           MT-TI\n",
       "  ENSG00000210107           MT-TQ\n",
       "  ENSG00000210112           MT-TM\n",
       "  ENSG00000198763          MT-ND2\n",
       "  ENSG00000210117           MT-TW\n",
       "  ENSG00000210127           MT-TA\n",
       "  ENSG00000210135           MT-TN\n",
       "  ENSG00000210140           MT-TC\n",
       "  ENSG00000210144           MT-TY\n",
       "  ENSG00000198804          MT-CO1\n",
       "  ENSG00000210151          MT-TS1\n",
       "  ENSG00000210154           MT-TD\n",
       "  ENSG00000198712          MT-CO2\n",
       "  ENSG00000210156           MT-TK\n",
       "  ENSG00000228253         MT-ATP8\n",
       "  ENSG00000198899         MT-ATP6\n",
       "  ENSG00000198938          MT-CO3\n",
       "  ENSG00000210164           MT-TG\n",
       "  ENSG00000198840          MT-ND3\n",
       "  ENSG00000210174           MT-TR\n",
       "  ENSG00000212907         MT-ND4L\n",
       "  ENSG00000198886          MT-ND4\n",
       "  ENSG00000210176           MT-TH\n",
       "  ENSG00000210184          MT-TS2\n",
       "  ENSG00000210191          MT-TL2\n",
       "  ENSG00000198786          MT-ND5\n",
       "  ENSG00000198695          MT-ND6\n",
       "  ENSG00000210194           MT-TE\n",
       "  ENSG00000198727          MT-CYB\n",
       "  ENSG00000210195           MT-TT\n",
       "  ENSG00000210196           MT-TP\n",
       "  ENSG00000278457         5S_rRNA\n",
       "  ENSG00000280663          PCMTD2\n",
       "  ENSG00000262826           INTS3\n",
       "  ENSG00000273947         KIR2DL3\n",
       "  ENSG00000278294       5_8S_rRNA\n",
       "  ENSG00000276779         KIR2DL4\n",
       "  ENSG00000274882       LINC02109\n",
       "  ENSG00000273735         KIR3DL2\n",
       "  ENSG00000275717         KIR3DL1\n",
       "  ENSG00000276379         KIR3DL1\n",
       "  ENSG00000276433         KIR3DL3\n",
       "  ENSG00000275442          LILRP2\n",
       "  ENSG00000274692         KIR2DL1\n",
       "                         ...     \n",
       "  ENSG00000230424        EMC1-AS1\n",
       "  ENSG00000077549           CAPZB\n",
       "  ENSG00000173436         MICOS10\n",
       "  ENSG00000201609        RNU4-28P\n",
       "  ENSG00000235185      MICOS10-DT\n",
       "  ENSG00000158747            NBL1\n",
       "  ENSG00000270136    MICOS10-NBL1\n",
       "  ENSG00000158748            HTR6\n",
       "  ENSG00000020633           RUNX3\n",
       "  ENSG00000229162       RUNX3-AS1\n",
       "  ENSG00000264371         MIR4425\n",
       "  ENSG00000285823       LINC02793\n",
       "  ENSG00000070831           CDC42\n",
       "  ENSG00000291072         CROCCP2\n",
       "  ENSG00000268869           ESPNP\n",
       "  ENSG00000231507       LINC01353\n",
       "  ENSG00000202300       RNU6-487P\n",
       "  ENSG00000122176            FMOD\n",
       "  ENSG00000271588         LARP7P1\n",
       "  ENSG00000211451          GNRHR2\n",
       "  ENSG00000233396       LINC01719\n",
       "  ENSG00000277406        SEC22B4P\n",
       "  ENSG00000273768        RNVU1-29\n",
       "  ENSG00000274428        RNVU1-25\n",
       "  ENSG00000274408       RNA5SP536\n",
       "  ENSG00000276975          HYDIN2\n",
       "  ENSG00000131781            FMO5\n",
       "  ENSG00000226015          CCT8P1\n",
       "  ENSG00000236806        RPL7AP15\n",
       "  ENSG00000131778           CHD1L\n",
       "  ENSG00000227947       LINC01738\n",
       "  ENSG00000269113         TRABD2B\n",
       "  ENSG00000226133       LINC02794\n",
       "  ENSG00000237180        CYP46A4P\n",
       "  ENSG00000242267         SKINT1L\n",
       "  ENSG00000117834          SLC5A9\n",
       "  ENSG00000132122          SPATA6\n",
       "  ENSG00000224986        PPP1R8P1\n",
       "  ENSG00000060718         COL11A1\n",
       "  ENSG00000234257          SOD2P1\n",
       "  ENSG00000135837          CEP350\n",
       "  ENSG00000117152            RGS4\n",
       "  ENSG00000085832           EPS15\n",
       "  ENSG00000227070       EPS15-AS1\n",
       "  ENSG00000227742          CALR4P\n",
       "  ENSG00000162543          UBXN10\n",
       "  ENSG00000134686            PHC2\n",
       "  ENSG00000159023           EPB41\n",
       "  ENSG00000198216         CACNA1E\n",
       "  ENSG00000159388            BTG2\n",
       "  Name: symb, Length: 46761, dtype: object},\n",
       " 'entr': {'ensg': entr\n",
       "  4535                                           ENSG00000198888\n",
       "  4536                                           ENSG00000198763\n",
       "  4512                                           ENSG00000198804\n",
       "  113219467                                      ENSG00000210151\n",
       "  4513                                           ENSG00000198712\n",
       "  4509                                           ENSG00000228253\n",
       "  4508                                           ENSG00000198899\n",
       "  4514                                           ENSG00000198938\n",
       "  4537                                           ENSG00000198840\n",
       "  4539                                           ENSG00000212907\n",
       "  4538                                           ENSG00000198886\n",
       "  4540                                           ENSG00000198786\n",
       "  4541                                           ENSG00000198695\n",
       "  4519                                           ENSG00000198727\n",
       "  102724250                                      ENSG00000271254\n",
       "  124907156                                      ENSG00000278294\n",
       "  124907485                                      ENSG00000278294\n",
       "  124908250                                      ENSG00000278294\n",
       "  124900573                                      ENSG00000278152\n",
       "  124900574                                      ENSG00000275946\n",
       "  124900572                                      ENSG00000276686\n",
       "  100288966                                      ENSG00000277630\n",
       "  504191                                         ENSG00000262191\n",
       "  124905334                                      ENSG00000278625\n",
       "  100996750                                      ENSG00000266286\n",
       "  100008587                                      ENSG00000274917\n",
       "  727764                                         ENSG00000274847\n",
       "  101929829                                      ENSG00000272000\n",
       "  504190                                         ENSG00000281038\n",
       "  504189                                         ENSG00000262315\n",
       "  124903857                                      ENSG00000268674\n",
       "  124905556                                      ENSG00000268674\n",
       "  124905693                                      ENSG00000268674\n",
       "  124905699                                      ENSG00000268674\n",
       "  109864274                                      ENSG00000276700\n",
       "  100293534                                      ENSG00000233312\n",
       "  105379627                                      ENSG00000282515\n",
       "  2952                                           ENSG00000277656\n",
       "  730394                                         ENSG00000274675\n",
       "  440225                                         ENSG00000290539\n",
       "  102723407                                      ENSG00000275063\n",
       "  100653049                                      ENSG00000262748\n",
       "  83867                                          ENSG00000237048\n",
       "  100101120                                      ENSG00000147761\n",
       "  84672                                          ENSG00000131538\n",
       "  252955                                         ENSG00000239225\n",
       "  246122                                         ENSG00000147753\n",
       "  9081                                           ENSG00000169789\n",
       "  252953                                         ENSG00000228890\n",
       "  8287                                           ENSG00000114374\n",
       "                                     ...                        \n",
       "  9172                           ENSG00000274137|ENSG00000036448\n",
       "  91746                          ENSG00000275272|ENSG00000083896\n",
       "  92126                          ENSG00000262102|ENSG00000171451\n",
       "  9223                           ENSG00000282956|ENSG00000151276\n",
       "  92259                          ENSG00000278461|ENSG00000134056\n",
       "  9228         ENSG00000282103|ENSG00000282152|ENSG0000027416...\n",
       "  9231                           ENSG00000274429|ENSG00000151208\n",
       "  9258                           ENSG00000285022|ENSG00000147324\n",
       "  9271                           ENSG00000275051|ENSG00000125207\n",
       "  9277         ENSG00000226916|ENSG00000236222|ENSG0000020422...\n",
       "  9278         ENSG00000206280|ENSG00000229253|ENSG0000022778...\n",
       "  92815                          ENSG00000284841|ENSG00000181218\n",
       "  9284                           ENSG00000281994|ENSG00000183426\n",
       "  93100                          ENSG00000278488|ENSG00000147813\n",
       "  932                            ENSG00000284903|ENSG00000149516\n",
       "  9326                           ENSG00000278574|ENSG00000273611\n",
       "  93432                          ENSG00000278563|ENSG00000257743\n",
       "  93589                          ENSG00000284953|ENSG00000151062\n",
       "  9362                           ENSG00000285221|ENSG00000100884\n",
       "  9374         ENSG00000168452|ENSG00000206256|ENSG0000022760...\n",
       "  93974                          ENSG00000285390|ENSG00000130770\n",
       "  94059        ENSG00000274495|ENSG00000278312|ENSG0000027357...\n",
       "  94104                          ENSG00000263141|ENSG00000159086\n",
       "  9437         ENSG00000277334|ENSG00000276450|ENSG0000027552...\n",
       "  9466                           ENSG00000288185|ENSG00000104998\n",
       "  9501           ENSG00000282013|ENSG00000262334|ENSG00000181031\n",
       "  9509                           ENSG00000283802|ENSG00000087116\n",
       "  9560         ENSG00000282604|ENSG00000275313|ENSG0000027612...\n",
       "  9564                           ENSG00000285460|ENSG00000050820\n",
       "  9639                           ENSG00000274726|ENSG00000104728\n",
       "  9651                           ENSG00000276429|ENSG00000149527\n",
       "  9656         ENSG00000225589|ENSG00000224587|ENSG0000023401...\n",
       "  9665                           ENSG00000277140|ENSG00000166783\n",
       "  9692                           ENSG00000100890|ENSG00000258790\n",
       "  9710           ENSG00000279389|ENSG00000282735|ENSG00000166398\n",
       "  9727                           ENSG00000275338|ENSG00000090565\n",
       "  9744                           ENSG00000288169|ENSG00000072818\n",
       "  9746                           ENSG00000288427|ENSG00000139182\n",
       "  9782                           ENSG00000015479|ENSG00000280987\n",
       "  9794                           ENSG00000283780|ENSG00000161021\n",
       "  9811                           ENSG00000282825|ENSG00000134030\n",
       "  9824                           ENSG00000275568|ENSG00000198826\n",
       "  9831                           ENSG00000276340|ENSG00000183309\n",
       "  9834                           ENSG00000277059|ENSG00000226777\n",
       "  9842           ENSG00000276358|ENSG00000277111|ENSG00000225190\n",
       "  9859                           ENSG00000276725|ENSG00000143702\n",
       "  9884                           ENSG00000278742|ENSG00000176681\n",
       "  9920                           ENSG00000273645|ENSG00000176595\n",
       "  9985                           ENSG00000285007|ENSG00000100918\n",
       "  9994                           ENSG00000288475|ENSG00000118412\n",
       "  Length: 27206, dtype: object,\n",
       "  'symb': entr\n",
       "  4535                                                    MT-ND1\n",
       "  4536                                                    MT-ND2\n",
       "  4512                                                    MT-CO1\n",
       "  113219467                                               MT-TS1\n",
       "  4513                                                    MT-CO2\n",
       "  4509                                                   MT-ATP8\n",
       "  4508                                                   MT-ATP6\n",
       "  4514                                                    MT-CO3\n",
       "  4537                                                    MT-ND3\n",
       "  4539                                                   MT-ND4L\n",
       "  4538                                                    MT-ND4\n",
       "  4540                                                    MT-ND5\n",
       "  4541                                                    MT-ND6\n",
       "  4519                                                    MT-CYB\n",
       "  55251                                                   PCMTD2\n",
       "  65123                                                    INTS3\n",
       "  3804                                                   KIR2DL3\n",
       "  124907156                                            5_8S_rRNA\n",
       "  124907485                                            5_8S_rRNA\n",
       "  124908250                                            5_8S_rRNA\n",
       "  3805                                                   KIR2DL4\n",
       "  124900568                                              KIR2DL4\n",
       "  3812                                                   KIR3DL2\n",
       "  3811                                                   KIR3DL1\n",
       "  115653                                                 KIR3DL3\n",
       "  79166                                                   LILRP2\n",
       "  4987                                                     OPRL1\n",
       "  2832                                                    NPBWR2\n",
       "  3809                                                   KIR2DS4\n",
       "  4661                                                      MYT1\n",
       "  9437                                                      NCR1\n",
       "  100132285                                              KIR2DS2\n",
       "  124900573                                              KIR2DS2\n",
       "  124900575                                              KIR2DS2\n",
       "  3813                                                   KIR3DS1\n",
       "  3803                                                   KIR2DL2\n",
       "  3808                                                   KIR2DS3\n",
       "  339822                                               LINC01115\n",
       "  2204                                                      FCAR\n",
       "  3810                                                   KIR2DS5\n",
       "  124900569                                             KIR2DL5A\n",
       "  196385                                                  DNAH10\n",
       "  124900574                                             KIR2DL5B\n",
       "  80212                                                   CCDC92\n",
       "  57459                                                  GATAD2B\n",
       "  11000                                                  SLC27A3\n",
       "  3806                                                   KIR2DS1\n",
       "  80264                                                   ZNF430\n",
       "  124900572                                             KIR2DL5A\n",
       "  7639                                                     ZNF85\n",
       "                                     ...                        \n",
       "  3802                                           KIR2DL1|KIR2DS1\n",
       "  392188                                         USP17L4|USP17L8\n",
       "  3963                                            LGALS7B|LGALS7\n",
       "  401447                                         USP17L2|USP17L1\n",
       "  414060                                          TBC1D3C|TBC1D3\n",
       "  414062                                           CCL3L1|CCL3L3\n",
       "  440243                                    GOLGA6L22|GOLGA6L24P\n",
       "  441327                                         FAM90A7|FAM90A9\n",
       "  445347                                              TRGC1|TARP\n",
       "  474152                                         TTTY17A|TTTY17B\n",
       "  497190                                         CLEC18C|CLEC18B\n",
       "  503614                                       DEFB107B|DEFB107A\n",
       "  51326                                            ARL17B|ARL17A\n",
       "  548596                                           CKMT1B|CKMT1A\n",
       "  552900                                            BOLA2B|BOLA2\n",
       "  553128                                        KIR2DL5B|KIR2DS3\n",
       "  554313       H4C1|H4C4|H4C13|H4C6|H4C3|H4C8|H4C11|H4C12|H4C...\n",
       "  5554                                                 PRR4|PRH1\n",
       "  55894                                        DEFB103B|DEFB103A\n",
       "  57292                                         KIR2DL5A|KIR2DS5\n",
       "  6349                                             CCL3L1|CCL3L3\n",
       "  641367                                         CCNYL6|BRI3BPP1\n",
       "  641776                                 SPDYE14|SPDYE13|SPDYE15\n",
       "  642799                                    NPIPA3|NPIPA1|NPIPA2\n",
       "  643707                                      GOLGA6L10|GOLGA6L4\n",
       "  643836                                              ZFP62|HEIH\n",
       "  643862                   SPDYE9|SPDYE11|SPDYE17|SPDYE10|SPDYE8\n",
       "  643909                   SPDYE9|SPDYE11|SPDYE17|SPDYE10|SPDYE8\n",
       "  645359                                       PRAMEF25|PRAMEF26\n",
       "  645651                                        FAM90A9|FAM90A14\n",
       "  646066                                        TAF11L5|TAF11L10\n",
       "  646743                                         PRSS40B|PRSS40A\n",
       "  653125                                         GOLGA8T|GOLGA8K\n",
       "  653166                                             OR1D5|OR1D4\n",
       "  653247                                               PRB1|PRB2\n",
       "  653499                                          LGALS7B|LGALS7\n",
       "  653550             TP53TG3B|TP53TG3E|TP53TG3|TP53TG3F|TP53TG3C\n",
       "  653784                                             MZT2A|MZT2B\n",
       "  6606                                                 SMN2|SMN1\n",
       "  727856                                        DDX11L16|DDX11L2\n",
       "  727866                                         FAM156A|FAM156B\n",
       "  728047                                         GOLGA8Q|GOLGA8O\n",
       "  728340                                          GTF2H2|GTF2H2C\n",
       "  728656                                          DMRTC1B|DMRTC1\n",
       "  728689                                            EIF3CL|EIF3C\n",
       "  729873                                          TBC1D3L|TBC1D3\n",
       "  79008                                              SLX1A|SLX1B\n",
       "  81399                                      OR4F3|OR4F29|OR4F16\n",
       "  8293                                             SERF1B|SERF1A\n",
       "  89838                                            ULK4P2|ULK4P1\n",
       "  Length: 25879, dtype: object},\n",
       " 'symb': {'ensg': MT-TF                   ENSG00000210049\n",
       "  MT-RNR1                 ENSG00000211459\n",
       "  MT-TV                   ENSG00000210077\n",
       "  MT-RNR2                 ENSG00000210082\n",
       "  MT-TL1                  ENSG00000209082\n",
       "  MT-ND1                  ENSG00000198888\n",
       "  MT-TI                   ENSG00000210100\n",
       "  MT-TQ                   ENSG00000210107\n",
       "  MT-TM                   ENSG00000210112\n",
       "  MT-ND2                  ENSG00000198763\n",
       "  MT-TW                   ENSG00000210117\n",
       "  MT-TA                   ENSG00000210127\n",
       "  MT-TN                   ENSG00000210135\n",
       "  MT-TC                   ENSG00000210140\n",
       "  MT-TY                   ENSG00000210144\n",
       "  MT-CO1                  ENSG00000198804\n",
       "  MT-TS1                  ENSG00000210151\n",
       "  MT-TD                   ENSG00000210154\n",
       "  MT-CO2                  ENSG00000198712\n",
       "  MT-TK                   ENSG00000210156\n",
       "  MT-ATP8                 ENSG00000228253\n",
       "  MT-ATP6                 ENSG00000198899\n",
       "  MT-CO3                  ENSG00000198938\n",
       "  MT-TG                   ENSG00000210164\n",
       "  MT-ND3                  ENSG00000198840\n",
       "  MT-TR                   ENSG00000210174\n",
       "  MT-ND4L                 ENSG00000212907\n",
       "  MT-ND4                  ENSG00000198886\n",
       "  MT-TH                   ENSG00000210176\n",
       "  MT-TS2                  ENSG00000210184\n",
       "  MT-TL2                  ENSG00000210191\n",
       "  MT-ND5                  ENSG00000198786\n",
       "  MT-ND6                  ENSG00000198695\n",
       "  MT-TE                   ENSG00000210194\n",
       "  MT-CYB                  ENSG00000198727\n",
       "  MT-TT                   ENSG00000210195\n",
       "  MT-TP                   ENSG00000210196\n",
       "  OR9G9                   ENSG00000262191\n",
       "  RNA5-8SN5               ENSG00000274917\n",
       "  MAFIP                   ENSG00000274847\n",
       "  OR8U9                   ENSG00000281038\n",
       "  OR8U8                   ENSG00000262315\n",
       "  PRAMEF22                ENSG00000276816\n",
       "  RNA5-8SN4               ENSG00000276700\n",
       "  C4B_2                   ENSG00000233312\n",
       "  TAS2R45                 ENSG00000261936\n",
       "  GSTT1                   ENSG00000277656\n",
       "  GTF2H2C_2               ENSG00000274675\n",
       "  HLA-DRB2                ENSG00000227442\n",
       "  PRSS3P2                 ENSG00000282667\n",
       "                               ...       \n",
       "  MIO10                   ENSG00000173436\n",
       "  RP5-1056L3.2            ENSG00000173436\n",
       "  D1S1733E                ENSG00000158747\n",
       "  DAND1                   ENSG00000158747\n",
       "  NB                      ENSG00000158747\n",
       "  NO3                     ENSG00000158747\n",
       "  MINOS1-NBL1             ENSG00000270136\n",
       "  5-HT6                   ENSG00000158748\n",
       "  5-HT6R                  ENSG00000158748\n",
       "  AML2                    ENSG00000020633\n",
       "  CBFA3                   ENSG00000020633\n",
       "  PEBP2A3                 ENSG00000020633\n",
       "  hsa-mir-4425            ENSG00000264371\n",
       "  CDC42Hs                 ENSG00000070831\n",
       "  G25K                    ENSG00000070831\n",
       "  SLRR2E                  ENSG00000122176\n",
       "  HYDINP1                 ENSG00000276975\n",
       "  TIKI2                   ENSG00000269113\n",
       "  CYP46A-se1[12:13:14]    ENSG00000237180\n",
       "  BTN12                   ENSG00000242267\n",
       "  SKINTL                  ENSG00000242267\n",
       "  SKINTP                  ENSG00000242267\n",
       "  SGLT4                   ENSG00000117834\n",
       "  FLJ10007                ENSG00000132122\n",
       "  SRF-1                   ENSG00000132122\n",
       "  SRF1                    ENSG00000132122\n",
       "  PPP1R8P                 ENSG00000224986\n",
       "  CO11A1                  ENSG00000060718\n",
       "  COLL6                   ENSG00000060718\n",
       "  DFNA37                  ENSG00000060718\n",
       "  STL2                    ENSG00000060718\n",
       "  CAP350                  ENSG00000135837\n",
       "  KIAA0480                ENSG00000135837\n",
       "  SCZD9                   ENSG00000117152\n",
       "  AF-1P                   ENSG00000085832\n",
       "  MLLT5                   ENSG00000085832\n",
       "  FLJ25429                ENSG00000162543\n",
       "  UBXD3                   ENSG00000162543\n",
       "  EDR2                    ENSG00000134686\n",
       "  HPH2                    ENSG00000134686\n",
       "  4.1R                    ENSG00000159023\n",
       "  EL1                     ENSG00000159023\n",
       "  BII                     ENSG00000198216\n",
       "  CACH6                   ENSG00000198216\n",
       "  CACNL1A6                ENSG00000198216\n",
       "  Cav2.3                  ENSG00000198216\n",
       "  APRO1                   ENSG00000159388\n",
       "  MGC126063               ENSG00000159388\n",
       "  MGC126064               ENSG00000159388\n",
       "  TIS21                   ENSG00000159388\n",
       "  Length: 92407, dtype: object,\n",
       "  'entr': MT-ND1                    4535\n",
       "  MT-ND2                    4536\n",
       "  MT-CO1                    4512\n",
       "  MT-TS1               113219467\n",
       "  MT-CO2                    4513\n",
       "  MT-ATP8                   4509\n",
       "  MT-ATP6                   4508\n",
       "  MT-CO3                    4514\n",
       "  MT-ND3                    4537\n",
       "  MT-ND4L                   4539\n",
       "  MT-ND4                    4538\n",
       "  MT-ND5                    4540\n",
       "  MT-ND6                    4541\n",
       "  MT-CYB                    4519\n",
       "  PCMTD2                   55251\n",
       "  INTS3                    65123\n",
       "  KIR2DL3                   3804\n",
       "  KIR3DL2                   3812\n",
       "  KIR3DL1                   3811\n",
       "  KIR3DL3                 115653\n",
       "  LILRP2                   79166\n",
       "  KIR2DL1                   3802\n",
       "  OPRL1                     4987\n",
       "  NPBWR2                    2832\n",
       "  KIR2DS4                   3809\n",
       "  MYT1                      4661\n",
       "  NCR1                      9437\n",
       "  KIR3DS1                   3813\n",
       "  KIR2DL2                   3803\n",
       "  LINC01115               339822\n",
       "  FCAR                      2204\n",
       "  DNAH10                  196385\n",
       "  CCDC92                   80212\n",
       "  GATAD2B                  57459\n",
       "  SLC27A3                  11000\n",
       "  ZNF430                   80264\n",
       "  ZNF85                     7639\n",
       "  ZNF66                     7617\n",
       "  KRT20                    54474\n",
       "  OR9G4                   283189\n",
       "  KRTAP3-1                 83896\n",
       "  KRTAP3-2                 83897\n",
       "  KRTAP4-9             100132386\n",
       "  OR9G1                   390174\n",
       "  KRTAP2-4                 85294\n",
       "  OR9G9                   504191\n",
       "  LINC02735            101927120\n",
       "  KRT23                    25984\n",
       "  ZNF43                     7594\n",
       "  KRTAP9-9                 81870\n",
       "                       ...      \n",
       "  SLRR2A                    5549\n",
       "  MXRA1                      493\n",
       "  PMCA4                      493\n",
       "  C1orf151                440574\n",
       "  FLJ36999                440574\n",
       "  Mic10                   440574\n",
       "  MINOS1                  440574\n",
       "  MIO10                   440574\n",
       "  RP5-1056L3.2            440574\n",
       "  D1S1733E        4681|100532736\n",
       "  DAND1           4681|100532736\n",
       "  NB              4681|100532736\n",
       "  NO3             4681|100532736\n",
       "  5-HT6                     3362\n",
       "  5-HT6R                    3362\n",
       "  AML2                       864\n",
       "  CBFA3                      864\n",
       "  PEBP2A3                    864\n",
       "  hsa-mir-4425         100616365\n",
       "  CDC42Hs                    998\n",
       "  G25K                       998\n",
       "  SLRR2E                    2331\n",
       "  TIKI2                   388630\n",
       "  SGLT4                   200010\n",
       "  FLJ10007                 54558\n",
       "  SRF-1                    54558\n",
       "  SRF1                     54558\n",
       "  CO11A1                    1301\n",
       "  COLL6                     1301\n",
       "  DFNA37                    1301\n",
       "  STL2                      1301\n",
       "  CAP350                    9857\n",
       "  KIAA0480                  9857\n",
       "  SCZD9                     5999\n",
       "  AF-1P                     2060\n",
       "  MLLT5                     2060\n",
       "  FLJ25429                127733\n",
       "  UBXD3                   127733\n",
       "  EDR2                      1912\n",
       "  HPH2                      1912\n",
       "  4.1R                      2035\n",
       "  EL1                       2035\n",
       "  BII                        777\n",
       "  CACH6                      777\n",
       "  CACNL1A6                   777\n",
       "  Cav2.3                     777\n",
       "  APRO1                     7832\n",
       "  MGC126063                 7832\n",
       "  MGC126064                 7832\n",
       "  TIS21                     7832\n",
       "  Length: 71297, dtype: object}}"
      ]
     },
     "execution_count": 185,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tempvar"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 183,
   "id": "55c3f003",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T15:23:57.175666Z",
     "start_time": "2022-12-29T15:23:50.725025Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ensg\n",
       "ENSG00000000003         TSPAN6\n",
       "ENSG00000000005           TNMD\n",
       "ENSG00000000419           DPM1\n",
       "ENSG00000000457          SCYL3\n",
       "ENSG00000000460       C1orf112\n",
       "ENSG00000000938            FGR\n",
       "ENSG00000000971            CFH\n",
       "ENSG00000001036          FUCA2\n",
       "ENSG00000001084           GCLC\n",
       "ENSG00000001167           NFYA\n",
       "ENSG00000001460          STPG1\n",
       "ENSG00000001461         NIPAL3\n",
       "ENSG00000001497          LAS1L\n",
       "ENSG00000001561          ENPP4\n",
       "ENSG00000001617         SEMA3F\n",
       "ENSG00000001626           CFTR\n",
       "ENSG00000001629         ANKIB1\n",
       "ENSG00000001630        CYP51A1\n",
       "ENSG00000001631          KRIT1\n",
       "ENSG00000002016          RAD52\n",
       "ENSG00000002079          MYH16\n",
       "ENSG00000002330            BAD\n",
       "ENSG00000002549           LAP3\n",
       "ENSG00000002586           CD99\n",
       "ENSG00000002587         HS3ST1\n",
       "ENSG00000002726           AOC1\n",
       "ENSG00000002745          WNT16\n",
       "ENSG00000002746          HECW1\n",
       "ENSG00000002822         MAD1L1\n",
       "ENSG00000002834          LASP1\n",
       "ENSG00000002919          SNX11\n",
       "ENSG00000002933       TMEM176A\n",
       "ENSG00000003056           M6PR\n",
       "ENSG00000003096         KLHL13\n",
       "ENSG00000003137        CYP26B1\n",
       "ENSG00000003147           ICA1\n",
       "ENSG00000003249         DBNDD1\n",
       "ENSG00000003393           ALS2\n",
       "ENSG00000003400         CASP10\n",
       "ENSG00000003402          CFLAR\n",
       "ENSG00000003436           TFPI\n",
       "ENSG00000003509        NDUFAF7\n",
       "ENSG00000003756           RBM5\n",
       "ENSG00000003987          MTMR7\n",
       "ENSG00000003989         SLC7A2\n",
       "ENSG00000004059           ARF5\n",
       "ENSG00000004139          SARM1\n",
       "ENSG00000004142        POLDIP2\n",
       "ENSG00000004399         PLXND1\n",
       "ENSG00000004455            AK2\n",
       "                      ...     \n",
       "ENSG00000291252            nan\n",
       "ENSG00000291253            nan\n",
       "ENSG00000291254            nan\n",
       "ENSG00000291255            nan\n",
       "ENSG00000291256            nan\n",
       "ENSG00000291257            nan\n",
       "ENSG00000291258            nan\n",
       "ENSG00000291259            nan\n",
       "ENSG00000291260            nan\n",
       "ENSG00000291261            nan\n",
       "ENSG00000291262            nan\n",
       "ENSG00000291263         SMG1P7\n",
       "ENSG00000291264            nan\n",
       "ENSG00000291265            nan\n",
       "ENSG00000291266         SMG1P5\n",
       "ENSG00000291267            nan\n",
       "ENSG00000291268            nan\n",
       "ENSG00000291269            nan\n",
       "ENSG00000291270            nan\n",
       "ENSG00000291271            nan\n",
       "ENSG00000291272            nan\n",
       "ENSG00000291273            nan\n",
       "ENSG00000291274            nan\n",
       "ENSG00000291275            nan\n",
       "ENSG00000291276            nan\n",
       "ENSG00000291277            nan\n",
       "ENSG00000291278            nan\n",
       "ENSG00000291279            nan\n",
       "ENSG00000291280    ANKRD20A11P\n",
       "ENSG00000291281       COL6A4P1\n",
       "ENSG00000291282            nan\n",
       "ENSG00000291283            nan\n",
       "ENSG00000291284            nan\n",
       "ENSG00000291285            nan\n",
       "ENSG00000291286            nan\n",
       "ENSG00000291287            nan\n",
       "ENSG00000291288            nan\n",
       "ENSG00000291289            nan\n",
       "ENSG00000291290            nan\n",
       "ENSG00000291291            nan\n",
       "ENSG00000291292            nan\n",
       "ENSG00000291293            nan\n",
       "ENSG00000291294            nan\n",
       "ENSG00000291295            nan\n",
       "ENSG00000291296            nan\n",
       "ENSG00000291297            nan\n",
       "ENSG00000291298            nan\n",
       "ENSG00000291299            nan\n",
       "ENSG00000291300        PRSS30P\n",
       "ENSG00000291301            nan\n",
       "Length: 69292, dtype: object"
      ]
     },
     "execution_count": 183,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idm._sources[0]._data.groupby('ensg').apply(lambda x: '|'.join(map(str,x.symb.unique())))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 176,
   "id": "00b47bac",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T15:23:01.777624Z",
     "start_time": "2022-12-29T15:23:01.774551Z"
    }
   },
   "outputs": [],
   "source": [
    "tempvar = _"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 155,
   "id": "0742d73a",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T00:52:43.053945Z",
     "start_time": "2022-12-29T00:52:43.005835Z"
    }
   },
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "ensembl: invalid input ID type",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[155], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43midm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sources\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m1017\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mciao\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mENSG00000123374\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mA1BG\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mensgs\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msymb\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/Postdoc/Libs/biorosetta/main.py:47\u001b[0m, in \u001b[0;36mLocalSource.convert\u001b[0;34m(self, id_list, id_in, id_out)\u001b[0m\n\u001b[1;32m     46\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mconvert\u001b[39m(\u001b[38;5;28mself\u001b[39m, id_list, id_in, id_out):\n\u001b[0;32m---> 47\u001b[0m \tid_list \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msanitize\u001b[49m\u001b[43m(\u001b[49m\u001b[43mid_list\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mid_in\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mid_out\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     48\u001b[0m \t\u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_lookup[id_in][id_out]\u001b[38;5;241m.\u001b[39mreindex(id_list,fill_value\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fill_value)\n",
      "File \u001b[0;32m~/Postdoc/Libs/biorosetta/main.py:14\u001b[0m, in \u001b[0;36mSource.sanitize\u001b[0;34m(self, id_list, id_in, id_out)\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21msanitize\u001b[39m(\u001b[38;5;28mself\u001b[39m, id_list, id_in, id_out):\n\u001b[1;32m     13\u001b[0m \t\u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhas_id_in_type(id_in):\n\u001b[0;32m---> 14\u001b[0m \t\t\u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msource_id\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: invalid input ID type\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m     15\u001b[0m \t\u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhas_id_out_type(id_out):\n\u001b[1;32m     16\u001b[0m \t\t\u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msource_id\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: invalid output ID type\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
      "\u001b[0;31mValueError\u001b[0m: ensembl: invalid input ID type"
     ]
    }
   ],
   "source": [
    "idm._sources[0].convert(['1017','ciao',1,'ENSG00000123374','A1BG'], 'ensgs', 'symb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 135,
   "id": "1c3cd120",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T00:47:51.561339Z",
     "start_time": "2022-12-29T00:47:51.485426Z"
    }
   },
   "outputs": [],
   "source": [
    "tempvar = idm._sources[0]._data.fillna('N/A')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 148,
   "id": "083ad22d",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T00:49:04.844850Z",
     "start_time": "2022-12-29T00:49:04.766513Z"
    }
   },
   "outputs": [
    {
     "ename": "error",
     "evalue": "bad escape (end of pattern) at position 0",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31merror\u001b[0m                                     Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[148], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m tempvar[\u001b[43mtempvar\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msymb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcontains\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;130;43;01m\\\\\u001b[39;49;00m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m]\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/strings/accessor.py:129\u001b[0m, in \u001b[0;36mforbid_nonstring_types.<locals>._forbid_nonstring_types.<locals>.wrapper\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    124\u001b[0m     msg \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m    125\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCannot use .str.\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mfunc_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m with values of \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    126\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minferred dtype \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_inferred_dtype\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    127\u001b[0m     )\n\u001b[1;32m    128\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(msg)\n\u001b[0;32m--> 129\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/strings/accessor.py:1252\u001b[0m, in \u001b[0;36mStringMethods.contains\u001b[0;34m(self, pat, case, flags, na, regex)\u001b[0m\n\u001b[1;32m   1127\u001b[0m \u001b[38;5;129m@forbid_nonstring_types\u001b[39m([\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mbytes\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n\u001b[1;32m   1128\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcontains\u001b[39m(\u001b[38;5;28mself\u001b[39m, pat, case\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, flags\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m, na\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, regex\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m):\n\u001b[1;32m   1129\u001b[0m     \u001b[38;5;124mr\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m   1130\u001b[0m \u001b[38;5;124;03m    Test if pattern or regex is contained within a string of a Series or Index.\u001b[39;00m\n\u001b[1;32m   1131\u001b[0m \n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m   1250\u001b[0m \u001b[38;5;124;03m    dtype: bool\u001b[39;00m\n\u001b[1;32m   1251\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[0;32m-> 1252\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m regex \u001b[38;5;129;01mand\u001b[39;00m \u001b[43mre\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcompile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpat\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mgroups:\n\u001b[1;32m   1253\u001b[0m         warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m   1254\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mThis pattern is interpreted as a regular expression, and has \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m   1255\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmatch groups. To actually get the groups, use str.extract.\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m   1256\u001b[0m             \u001b[38;5;167;01mUserWarning\u001b[39;00m,\n\u001b[1;32m   1257\u001b[0m             stacklevel\u001b[38;5;241m=\u001b[39mfind_stack_level(),\n\u001b[1;32m   1258\u001b[0m         )\n\u001b[1;32m   1260\u001b[0m     result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_data\u001b[38;5;241m.\u001b[39marray\u001b[38;5;241m.\u001b[39m_str_contains(pat, case, flags, na, regex)\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/re.py:251\u001b[0m, in \u001b[0;36mcompile\u001b[0;34m(pattern, flags)\u001b[0m\n\u001b[1;32m    249\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcompile\u001b[39m(pattern, flags\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m):\n\u001b[1;32m    250\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCompile a regular expression pattern, returning a Pattern object.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 251\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_compile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpattern\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mflags\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/re.py:303\u001b[0m, in \u001b[0;36m_compile\u001b[0;34m(pattern, flags)\u001b[0m\n\u001b[1;32m    301\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m sre_compile\u001b[38;5;241m.\u001b[39misstring(pattern):\n\u001b[1;32m    302\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mfirst argument must be string or compiled pattern\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 303\u001b[0m p \u001b[38;5;241m=\u001b[39m \u001b[43msre_compile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcompile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpattern\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mflags\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    304\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (flags \u001b[38;5;241m&\u001b[39m DEBUG):\n\u001b[1;32m    305\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(_cache) \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m _MAXCACHE:\n\u001b[1;32m    306\u001b[0m         \u001b[38;5;66;03m# Drop the oldest item\u001b[39;00m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/sre_compile.py:788\u001b[0m, in \u001b[0;36mcompile\u001b[0;34m(p, flags)\u001b[0m\n\u001b[1;32m    786\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m isstring(p):\n\u001b[1;32m    787\u001b[0m     pattern \u001b[38;5;241m=\u001b[39m p\n\u001b[0;32m--> 788\u001b[0m     p \u001b[38;5;241m=\u001b[39m \u001b[43msre_parse\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mparse\u001b[49m\u001b[43m(\u001b[49m\u001b[43mp\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mflags\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    789\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    790\u001b[0m     pattern \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/sre_parse.py:947\u001b[0m, in \u001b[0;36mparse\u001b[0;34m(str, flags, state)\u001b[0m\n\u001b[1;32m    944\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mparse\u001b[39m(\u001b[38;5;28mstr\u001b[39m, flags\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m, state\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[1;32m    945\u001b[0m     \u001b[38;5;66;03m# parse 're' pattern into list of (opcode, argument) tuples\u001b[39;00m\n\u001b[0;32m--> 947\u001b[0m     source \u001b[38;5;241m=\u001b[39m \u001b[43mTokenizer\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m    949\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m state \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m    950\u001b[0m         state \u001b[38;5;241m=\u001b[39m State()\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/sre_parse.py:233\u001b[0m, in \u001b[0;36mTokenizer.__init__\u001b[0;34m(self, string)\u001b[0m\n\u001b[1;32m    231\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mindex \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0\u001b[39m\n\u001b[1;32m    232\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mnext \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m--> 233\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__next\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/sre_parse.py:246\u001b[0m, in \u001b[0;36mTokenizer.__next\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    244\u001b[0m         char \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdecoded_string[index]\n\u001b[1;32m    245\u001b[0m     \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mIndexError\u001b[39;00m:\n\u001b[0;32m--> 246\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m error(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mbad escape (end of pattern)\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m    247\u001b[0m                     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstring, \u001b[38;5;28mlen\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstring) \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[1;32m    248\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mindex \u001b[38;5;241m=\u001b[39m index \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m    249\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mnext \u001b[38;5;241m=\u001b[39m char\n",
      "\u001b[0;31merror\u001b[0m: bad escape (end of pattern) at position 0"
     ]
    }
   ],
   "source": [
    "tempvar[tempvar.symb.str.contains('')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "id": "577c7eeb",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T00:30:17.075822Z",
     "start_time": "2022-12-29T00:30:15.649017Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-5...done.\n",
      "                  _id  _version     ensembl.gene notfound\n",
      "query                                                    \n",
      "1017             1017       2.0  ENSG00000123374      NaN\n",
      "ciao              NaN       NaN              NaN     True\n",
      "1                   1       2.0  ENSG00000121410      NaN\n",
      "ENSG00000123374  1017       2.0  ENSG00000123374      NaN\n",
      "A1BG              NaN       NaN              NaN     True\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "query\n",
       "1017               ENSG00000123374\n",
       "ciao                           N/A\n",
       "1                  ENSG00000121410\n",
       "ENSG00000123374    ENSG00000123374\n",
       "A1BG                           N/A\n",
       "Name: ensembl.gene, dtype: object"
      ]
     },
     "execution_count": 105,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mygene = m.MyGene()\n",
    "mygene.convert(['1017','ciao',1,'ENSG00000123374','A1BG'], 'entr', 'ensg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "id": "3c210aed",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T00:08:19.175037Z",
     "start_time": "2022-12-29T00:08:17.952373Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "entr\n",
       "1017               ENSG00000123374\n",
       "ciao                           N/A\n",
       "1                              N/A\n",
       "ENSG00000123374                N/A\n",
       "A1BG                           N/A\n",
       "dtype: object"
      ]
     },
     "execution_count": 79,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m.EnsemblBiomart().convert(['1017','ciao',1,'ENSG00000123374','A1BG'],'entr','ensg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "id": "893e2bba",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-29T00:30:32.985424Z",
     "start_time": "2022-12-29T00:30:31.567309Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "querying 1-1...done.\n"
     ]
    },
    {
     "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>_id</th>\n",
       "      <th>_version</th>\n",
       "      <th>ensembl.gene</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>query</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>ENSG00000121410</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      _id  _version     ensembl.gene\n",
       "query                               \n",
       "1       1         2  ENSG00000121410"
      ]
     },
     "execution_count": 106,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mygene.mg.getgenes([1], scopes='entrezgene', fields='ensembl.gene',\n",
    "    species='human', as_dataframe=True, returnall=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2319ff32",
   "metadata": {},
   "source": [
    "# NML"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "57500343",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:03:33.280448Z",
     "start_time": "2022-12-28T23:03:33.184544Z"
    }
   },
   "outputs": [],
   "source": [
    "temp1 = pd.read_table('/Users/reema/Postdoc/Libs/biorosetta/data/hgnc.tsv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "a0aa7ff1",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:03:36.112432Z",
     "start_time": "2022-12-28T23:03:35.975242Z"
    }
   },
   "outputs": [],
   "source": [
    "temp2 = pd.read_table('/Users/reema/Postdoc/Libs/biorosetta/data/ensembl.tsv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "c4edc5bc",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:04:24.940378Z",
     "start_time": "2022-12-28T23:04:24.926596Z"
    }
   },
   "outputs": [
    {
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      "text/plain": [
       "              ensg      entr      symb  synonym1    synonym2\n",
       "1  ENSG00000268895  503538.0  A1BG-AS1  FLJ23569  NCRNA00181\n",
       "2  ENSG00000268895  503538.0  A1BG-AS1  FLJ23569      A1BGAS\n",
       "3  ENSG00000268895  503538.0  A1BG-AS1  FLJ23569     A1BG-AS"
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     "metadata": {},
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    "temp1[temp1.ensg=='ENSG00000268895']"
   ]
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  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "d439817b",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:06:46.479917Z",
     "start_time": "2022-12-28T23:06:46.476161Z"
    }
   },
   "outputs": [],
   "source": [
    "pd.options.display.max_rows = 100\n",
    "pd.options.display.min_rows = 100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "40f3ed5f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:06:55.885785Z",
     "start_time": "2022-12-28T23:06:55.731372Z"
    }
   },
   "outputs": [
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       "      <td>A1BG-AS1</td>\n",
       "      <td>A1BGAS</td>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>ENSG00000268895</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ENSG00000268895</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
       "      <td>A1BGAS</td>\n",
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       "      <td>NCRNA00181</td>\n",
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       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>ENSG00000268895</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
       "      <td>A1BG-AS</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>A1BG-AS</td>\n",
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       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ENSG00000268895</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
       "      <td>A1BG-AS</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>A1BGAS</td>\n",
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       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>ENSG00000268895</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
       "      <td>A1BG-AS</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
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       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>ENSG00000268895</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>FLJ23569</td>\n",
       "      <td>A1BG-AS</td>\n",
       "      <td>503538.0</td>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>NCRNA00181</td>\n",
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       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
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       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
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       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
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       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
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       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
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       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
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       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ACF65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>ENSG00000148584</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>APOBEC1CF</td>\n",
       "      <td>NaN</td>\n",
       "      <td>29974.0</td>\n",
       "      <td>A1CF</td>\n",
       "      <td>ASP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>FWP007</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>CPAMD5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>FWP007</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>FWP007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>FWP007</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>S863-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>S863-7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>CPAMD5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>S863-7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>FWP007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>S863-7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>S863-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>CPAMD5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>CPAMD5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>CPAMD5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>FWP007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>ENSG00000175899</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>CPAMD5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>A2M</td>\n",
       "      <td>S863-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>ENSG00000245105</td>\n",
       "      <td>144571.0</td>\n",
       "      <td>A2M-AS1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>144571.0</td>\n",
       "      <td>A2M-AS1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>ENSG00000166535</td>\n",
       "      <td>144568.0</td>\n",
       "      <td>A2ML1</td>\n",
       "      <td>FLJ25179</td>\n",
       "      <td>CPAMD9</td>\n",
       "      <td>144568.0</td>\n",
       "      <td>A2ML1</td>\n",
       "      <td>CPAMD9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>ENSG00000166535</td>\n",
       "      <td>144568.0</td>\n",
       "      <td>A2ML1</td>\n",
       "      <td>FLJ25179</td>\n",
       "      <td>CPAMD9</td>\n",
       "      <td>144568.0</td>\n",
       "      <td>A2ML1</td>\n",
       "      <td>FLJ25179</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265306</th>\n",
       "      <td>ENSG00000291157</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265307</th>\n",
       "      <td>ENSG00000291158</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>57234.0</td>\n",
       "      <td>LINC00869</td>\n",
       "      <td>FAM91A2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265308</th>\n",
       "      <td>ENSG00000291158</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>388692.0</td>\n",
       "      <td>LINC00869</td>\n",
       "      <td>FAM91A2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265309</th>\n",
       "      <td>ENSG00000231827</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265310</th>\n",
       "      <td>ENSG00000291199</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>343052.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265311</th>\n",
       "      <td>ENSG00000228327</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265312</th>\n",
       "      <td>ENSG00000291215</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265313</th>\n",
       "      <td>ENSG00000291216</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265314</th>\n",
       "      <td>ENSG00000291217</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>731275.0</td>\n",
       "      <td>LINC01347</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265315</th>\n",
       "      <td>ENSG00000236957</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265316</th>\n",
       "      <td>ENSG00000291226</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>105371458.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265317</th>\n",
       "      <td>ENSG00000291232</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265318</th>\n",
       "      <td>ENSG00000215861</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265319</th>\n",
       "      <td>ENSG00000291233</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265320</th>\n",
       "      <td>ENSG00000291234</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265321</th>\n",
       "      <td>ENSG00000288982</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265322</th>\n",
       "      <td>ENSG00000284699</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265323</th>\n",
       "      <td>ENSG00000285053</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6905.0</td>\n",
       "      <td>TBCE</td>\n",
       "      <td>HRD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265324</th>\n",
       "      <td>ENSG00000285053</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6905.0</td>\n",
       "      <td>TBCE</td>\n",
       "      <td>KCS</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265325</th>\n",
       "      <td>ENSG00000285053</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6905.0</td>\n",
       "      <td>TBCE</td>\n",
       "      <td>KCS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265326</th>\n",
       "      <td>ENSG00000285053</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6905.0</td>\n",
       "      <td>TBCE</td>\n",
       "      <td>pac2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265327</th>\n",
       "      <td>ENSG00000226396</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265328</th>\n",
       "      <td>ENSG00000261025</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265329</th>\n",
       "      <td>ENSG00000291072</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>84809.0</td>\n",
       "      <td>CROCCP2</td>\n",
       "      <td>CROCCL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265330</th>\n",
       "      <td>ENSG00000290849</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265331</th>\n",
       "      <td>ENSG00000290850</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265332</th>\n",
       "      <td>ENSG00000290851</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265333</th>\n",
       "      <td>ENSG00000238142</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>105376805.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265334</th>\n",
       "      <td>ENSG00000290122</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265335</th>\n",
       "      <td>ENSG00000229652</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265336</th>\n",
       "      <td>ENSG00000290578</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265337</th>\n",
       "      <td>ENSG00000287978</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265338</th>\n",
       "      <td>ENSG00000277655</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265339</th>\n",
       "      <td>ENSG00000291242</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265340</th>\n",
       "      <td>ENSG00000289321</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265341</th>\n",
       "      <td>ENSG00000290557</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265342</th>\n",
       "      <td>ENSG00000274450</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265343</th>\n",
       "      <td>ENSG00000291243</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265344</th>\n",
       "      <td>ENSG00000237188</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265345</th>\n",
       "      <td>ENSG00000213226</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265346</th>\n",
       "      <td>ENSG00000223814</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265347</th>\n",
       "      <td>ENSG00000225028</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265348</th>\n",
       "      <td>ENSG00000231413</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265349</th>\n",
       "      <td>ENSG00000279096</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265350</th>\n",
       "      <td>ENSG00000223720</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265351</th>\n",
       "      <td>ENSG00000272491</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265352</th>\n",
       "      <td>ENSG00000279214</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265353</th>\n",
       "      <td>ENSG00000290466</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265354</th>\n",
       "      <td>ENSG00000291246</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265355</th>\n",
       "      <td>ENSG00000230864</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>265356 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   ensg    entr_x    symb_x   synonym1    synonym2  \\\n",
       "0       ENSG00000121410       1.0      A1BG        NaN         NaN   \n",
       "1       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569  NCRNA00181   \n",
       "2       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569  NCRNA00181   \n",
       "3       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569  NCRNA00181   \n",
       "4       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569  NCRNA00181   \n",
       "5       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569      A1BGAS   \n",
       "6       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569      A1BGAS   \n",
       "7       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569      A1BGAS   \n",
       "8       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569      A1BGAS   \n",
       "9       ENSG00000268895  503538.0  A1BG-AS1   FLJ23569     A1BG-AS   \n",
       "10      ENSG00000268895  503538.0  A1BG-AS1   FLJ23569     A1BG-AS   \n",
       "11      ENSG00000268895  503538.0  A1BG-AS1   FLJ23569     A1BG-AS   \n",
       "12      ENSG00000268895  503538.0  A1BG-AS1   FLJ23569     A1BG-AS   \n",
       "13      ENSG00000148584   29974.0      A1CF        ACF         NaN   \n",
       "14      ENSG00000148584   29974.0      A1CF        ACF         NaN   \n",
       "15      ENSG00000148584   29974.0      A1CF        ACF         NaN   \n",
       "16      ENSG00000148584   29974.0      A1CF        ACF         NaN   \n",
       "17      ENSG00000148584   29974.0      A1CF        ACF         NaN   \n",
       "18      ENSG00000148584   29974.0      A1CF        ASP         NaN   \n",
       "19      ENSG00000148584   29974.0      A1CF        ASP         NaN   \n",
       "20      ENSG00000148584   29974.0      A1CF        ASP         NaN   \n",
       "21      ENSG00000148584   29974.0      A1CF        ASP         NaN   \n",
       "22      ENSG00000148584   29974.0      A1CF        ASP         NaN   \n",
       "23      ENSG00000148584   29974.0      A1CF      ACF64         NaN   \n",
       "24      ENSG00000148584   29974.0      A1CF      ACF64         NaN   \n",
       "25      ENSG00000148584   29974.0      A1CF      ACF64         NaN   \n",
       "26      ENSG00000148584   29974.0      A1CF      ACF64         NaN   \n",
       "27      ENSG00000148584   29974.0      A1CF      ACF64         NaN   \n",
       "28      ENSG00000148584   29974.0      A1CF      ACF65         NaN   \n",
       "29      ENSG00000148584   29974.0      A1CF      ACF65         NaN   \n",
       "30      ENSG00000148584   29974.0      A1CF      ACF65         NaN   \n",
       "31      ENSG00000148584   29974.0      A1CF      ACF65         NaN   \n",
       "32      ENSG00000148584   29974.0      A1CF      ACF65         NaN   \n",
       "33      ENSG00000148584   29974.0      A1CF  APOBEC1CF         NaN   \n",
       "34      ENSG00000148584   29974.0      A1CF  APOBEC1CF         NaN   \n",
       "35      ENSG00000148584   29974.0      A1CF  APOBEC1CF         NaN   \n",
       "36      ENSG00000148584   29974.0      A1CF  APOBEC1CF         NaN   \n",
       "37      ENSG00000148584   29974.0      A1CF  APOBEC1CF         NaN   \n",
       "38      ENSG00000175899       2.0       A2M     FWP007         NaN   \n",
       "39      ENSG00000175899       2.0       A2M     FWP007         NaN   \n",
       "40      ENSG00000175899       2.0       A2M     FWP007         NaN   \n",
       "41      ENSG00000175899       2.0       A2M     S863-7         NaN   \n",
       "42      ENSG00000175899       2.0       A2M     S863-7         NaN   \n",
       "43      ENSG00000175899       2.0       A2M     S863-7         NaN   \n",
       "44      ENSG00000175899       2.0       A2M     CPAMD5         NaN   \n",
       "45      ENSG00000175899       2.0       A2M     CPAMD5         NaN   \n",
       "46      ENSG00000175899       2.0       A2M     CPAMD5         NaN   \n",
       "47      ENSG00000245105  144571.0   A2M-AS1        NaN         NaN   \n",
       "48      ENSG00000166535  144568.0     A2ML1   FLJ25179      CPAMD9   \n",
       "49      ENSG00000166535  144568.0     A2ML1   FLJ25179      CPAMD9   \n",
       "...                 ...       ...       ...        ...         ...   \n",
       "265306  ENSG00000291157       NaN       NaN        NaN         NaN   \n",
       "265307  ENSG00000291158       NaN       NaN        NaN         NaN   \n",
       "265308  ENSG00000291158       NaN       NaN        NaN         NaN   \n",
       "265309  ENSG00000231827       NaN       NaN        NaN         NaN   \n",
       "265310  ENSG00000291199       NaN       NaN        NaN         NaN   \n",
       "265311  ENSG00000228327       NaN       NaN        NaN         NaN   \n",
       "265312  ENSG00000291215       NaN       NaN        NaN         NaN   \n",
       "265313  ENSG00000291216       NaN       NaN        NaN         NaN   \n",
       "265314  ENSG00000291217       NaN       NaN        NaN         NaN   \n",
       "265315  ENSG00000236957       NaN       NaN        NaN         NaN   \n",
       "265316  ENSG00000291226       NaN       NaN        NaN         NaN   \n",
       "265317  ENSG00000291232       NaN       NaN        NaN         NaN   \n",
       "265318  ENSG00000215861       NaN       NaN        NaN         NaN   \n",
       "265319  ENSG00000291233       NaN       NaN        NaN         NaN   \n",
       "265320  ENSG00000291234       NaN       NaN        NaN         NaN   \n",
       "265321  ENSG00000288982       NaN       NaN        NaN         NaN   \n",
       "265322  ENSG00000284699       NaN       NaN        NaN         NaN   \n",
       "265323  ENSG00000285053       NaN       NaN        NaN         NaN   \n",
       "265324  ENSG00000285053       NaN       NaN        NaN         NaN   \n",
       "265325  ENSG00000285053       NaN       NaN        NaN         NaN   \n",
       "265326  ENSG00000285053       NaN       NaN        NaN         NaN   \n",
       "265327  ENSG00000226396       NaN       NaN        NaN         NaN   \n",
       "265328  ENSG00000261025       NaN       NaN        NaN         NaN   \n",
       "265329  ENSG00000291072       NaN       NaN        NaN         NaN   \n",
       "265330  ENSG00000290849       NaN       NaN        NaN         NaN   \n",
       "265331  ENSG00000290850       NaN       NaN        NaN         NaN   \n",
       "265332  ENSG00000290851       NaN       NaN        NaN         NaN   \n",
       "265333  ENSG00000238142       NaN       NaN        NaN         NaN   \n",
       "265334  ENSG00000290122       NaN       NaN        NaN         NaN   \n",
       "265335  ENSG00000229652       NaN       NaN        NaN         NaN   \n",
       "265336  ENSG00000290578       NaN       NaN        NaN         NaN   \n",
       "265337  ENSG00000287978       NaN       NaN        NaN         NaN   \n",
       "265338  ENSG00000277655       NaN       NaN        NaN         NaN   \n",
       "265339  ENSG00000291242       NaN       NaN        NaN         NaN   \n",
       "265340  ENSG00000289321       NaN       NaN        NaN         NaN   \n",
       "265341  ENSG00000290557       NaN       NaN        NaN         NaN   \n",
       "265342  ENSG00000274450       NaN       NaN        NaN         NaN   \n",
       "265343  ENSG00000291243       NaN       NaN        NaN         NaN   \n",
       "265344  ENSG00000237188       NaN       NaN        NaN         NaN   \n",
       "265345  ENSG00000213226       NaN       NaN        NaN         NaN   \n",
       "265346  ENSG00000223814       NaN       NaN        NaN         NaN   \n",
       "265347  ENSG00000225028       NaN       NaN        NaN         NaN   \n",
       "265348  ENSG00000231413       NaN       NaN        NaN         NaN   \n",
       "265349  ENSG00000279096       NaN       NaN        NaN         NaN   \n",
       "265350  ENSG00000223720       NaN       NaN        NaN         NaN   \n",
       "265351  ENSG00000272491       NaN       NaN        NaN         NaN   \n",
       "265352  ENSG00000279214       NaN       NaN        NaN         NaN   \n",
       "265353  ENSG00000290466       NaN       NaN        NaN         NaN   \n",
       "265354  ENSG00000291246       NaN       NaN        NaN         NaN   \n",
       "265355  ENSG00000230864       NaN       NaN        NaN         NaN   \n",
       "\n",
       "             entr_y     symb_y     synonym  \n",
       "0               1.0       A1BG         NaN  \n",
       "1          503538.0   A1BG-AS1     A1BG-AS  \n",
       "2          503538.0   A1BG-AS1      A1BGAS  \n",
       "3          503538.0   A1BG-AS1    FLJ23569  \n",
       "4          503538.0   A1BG-AS1  NCRNA00181  \n",
       "5          503538.0   A1BG-AS1     A1BG-AS  \n",
       "6          503538.0   A1BG-AS1      A1BGAS  \n",
       "7          503538.0   A1BG-AS1    FLJ23569  \n",
       "8          503538.0   A1BG-AS1  NCRNA00181  \n",
       "9          503538.0   A1BG-AS1     A1BG-AS  \n",
       "10         503538.0   A1BG-AS1      A1BGAS  \n",
       "11         503538.0   A1BG-AS1    FLJ23569  \n",
       "12         503538.0   A1BG-AS1  NCRNA00181  \n",
       "13          29974.0       A1CF         ACF  \n",
       "14          29974.0       A1CF       ACF64  \n",
       "15          29974.0       A1CF       ACF65  \n",
       "16          29974.0       A1CF   APOBEC1CF  \n",
       "17          29974.0       A1CF         ASP  \n",
       "18          29974.0       A1CF         ACF  \n",
       "19          29974.0       A1CF       ACF64  \n",
       "20          29974.0       A1CF       ACF65  \n",
       "21          29974.0       A1CF   APOBEC1CF  \n",
       "22          29974.0       A1CF         ASP  \n",
       "23          29974.0       A1CF         ACF  \n",
       "24          29974.0       A1CF       ACF64  \n",
       "25          29974.0       A1CF       ACF65  \n",
       "26          29974.0       A1CF   APOBEC1CF  \n",
       "27          29974.0       A1CF         ASP  \n",
       "28          29974.0       A1CF         ACF  \n",
       "29          29974.0       A1CF       ACF64  \n",
       "30          29974.0       A1CF       ACF65  \n",
       "31          29974.0       A1CF   APOBEC1CF  \n",
       "32          29974.0       A1CF         ASP  \n",
       "33          29974.0       A1CF         ACF  \n",
       "34          29974.0       A1CF       ACF64  \n",
       "35          29974.0       A1CF       ACF65  \n",
       "36          29974.0       A1CF   APOBEC1CF  \n",
       "37          29974.0       A1CF         ASP  \n",
       "38              2.0        A2M      CPAMD5  \n",
       "39              2.0        A2M      FWP007  \n",
       "40              2.0        A2M      S863-7  \n",
       "41              2.0        A2M      CPAMD5  \n",
       "42              2.0        A2M      FWP007  \n",
       "43              2.0        A2M      S863-7  \n",
       "44              2.0        A2M      CPAMD5  \n",
       "45              2.0        A2M      FWP007  \n",
       "46              2.0        A2M      S863-7  \n",
       "47         144571.0    A2M-AS1         NaN  \n",
       "48         144568.0      A2ML1      CPAMD9  \n",
       "49         144568.0      A2ML1    FLJ25179  \n",
       "...             ...        ...         ...  \n",
       "265306          NaN        NaN         NaN  \n",
       "265307      57234.0  LINC00869     FAM91A2  \n",
       "265308     388692.0  LINC00869     FAM91A2  \n",
       "265309          NaN        NaN         NaN  \n",
       "265310     343052.0        NaN         NaN  \n",
       "265311          NaN        NaN         NaN  \n",
       "265312          NaN        NaN         NaN  \n",
       "265313          NaN        NaN         NaN  \n",
       "265314     731275.0  LINC01347         NaN  \n",
       "265315          NaN        NaN         NaN  \n",
       "265316  105371458.0        NaN         NaN  \n",
       "265317          NaN        NaN         NaN  \n",
       "265318          NaN        NaN         NaN  \n",
       "265319          NaN        NaN         NaN  \n",
       "265320          NaN        NaN         NaN  \n",
       "265321          NaN        NaN         NaN  \n",
       "265322          NaN        NaN         NaN  \n",
       "265323       6905.0       TBCE         HRD  \n",
       "265324       6905.0       TBCE         KCS  \n",
       "265325       6905.0       TBCE        KCS1  \n",
       "265326       6905.0       TBCE        pac2  \n",
       "265327          NaN        NaN         NaN  \n",
       "265328          NaN        NaN         NaN  \n",
       "265329      84809.0    CROCCP2     CROCCL1  \n",
       "265330          NaN        NaN         NaN  \n",
       "265331          NaN        NaN         NaN  \n",
       "265332          NaN        NaN         NaN  \n",
       "265333  105376805.0        NaN         NaN  \n",
       "265334          NaN        NaN         NaN  \n",
       "265335          NaN        NaN         NaN  \n",
       "265336          NaN        NaN         NaN  \n",
       "265337          NaN        NaN         NaN  \n",
       "265338          NaN        NaN         NaN  \n",
       "265339          NaN        NaN         NaN  \n",
       "265340          NaN        NaN         NaN  \n",
       "265341          NaN        NaN         NaN  \n",
       "265342          NaN        NaN         NaN  \n",
       "265343          NaN        NaN         NaN  \n",
       "265344          NaN        NaN         NaN  \n",
       "265345          NaN        NaN         NaN  \n",
       "265346          NaN        NaN         NaN  \n",
       "265347          NaN        NaN         NaN  \n",
       "265348          NaN        NaN         NaN  \n",
       "265349          NaN        NaN         NaN  \n",
       "265350          NaN        NaN         NaN  \n",
       "265351          NaN        NaN         NaN  \n",
       "265352          NaN        NaN         NaN  \n",
       "265353          NaN        NaN         NaN  \n",
       "265354          NaN        NaN         NaN  \n",
       "265355          NaN        NaN         NaN  \n",
       "\n",
       "[265356 rows x 8 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "temp1.merge(temp2,left_on='ensg',right_on='ensg',how='outer')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "f416bd31",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T23:33:00.933875Z",
     "start_time": "2022-12-28T23:33:00.894386Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['MT-TF', '5S_rRNA', 'TTTY15', 'XKRY2']\n",
      "['MT-TF', '5S_rRNA', 'TTTY15', 'XKRYP7']\n"
     ]
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "7cd80703",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T17:59:05.248426Z",
     "start_time": "2022-12-27T17:59:05.186346Z"
    }
   },
   "outputs": [],
   "source": [
    "tempvar = sources[0]._lookup['ensg']['symb'].to_frame().merge(sources[1]._lookup['ensg']['symb'].to_frame(),left_on='ensg',right_on='ensg',how='outer')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "faadd7fa",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T18:00:26.185174Z",
     "start_time": "2022-12-27T18:00:26.165340Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "    .dataframe tbody tr th {\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>symb</th>\n",
       "      <th>0</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ensg</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000278457</th>\n",
       "      <td>5S_rRNA</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000280663</th>\n",
       "      <td>PCMTD2</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000262826</th>\n",
       "      <td>INTS3</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000273947</th>\n",
       "      <td>KIR2DL3</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000278294</th>\n",
       "      <td>5_8S_rRNA</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000226345</th>\n",
       "      <td>NaN</td>\n",
       "      <td>ZDHHC1P1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000243945</th>\n",
       "      <td>NaN</td>\n",
       "      <td>ZFAND2AP1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000275002</th>\n",
       "      <td>NaN</td>\n",
       "      <td>ZFAND2AP2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000233757</th>\n",
       "      <td>NaN</td>\n",
       "      <td>ZNF892</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000275120</th>\n",
       "      <td>NaN</td>\n",
       "      <td>ZSCAN2-AS1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7360 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      symb           0\n",
       "ensg                                  \n",
       "ENSG00000278457    5S_rRNA         NaN\n",
       "ENSG00000280663     PCMTD2         NaN\n",
       "ENSG00000262826      INTS3         NaN\n",
       "ENSG00000273947    KIR2DL3         NaN\n",
       "ENSG00000278294  5_8S_rRNA         NaN\n",
       "...                    ...         ...\n",
       "ENSG00000226345        NaN    ZDHHC1P1\n",
       "ENSG00000243945        NaN   ZFAND2AP1\n",
       "ENSG00000275002        NaN   ZFAND2AP2\n",
       "ENSG00000233757        NaN      ZNF892\n",
       "ENSG00000275120        NaN  ZSCAN2-AS1\n",
       "\n",
       "[7360 rows x 2 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tempvar[(tempvar.symb != tempvar[0])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "933d39c7",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T17:59:49.218043Z",
     "start_time": "2022-12-27T17:59:49.192370Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>symb</th>\n",
       "      <th>0</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ensg</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000244646</th>\n",
       "      <td>XKRY2</td>\n",
       "      <td>XKRYP7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000184624</th>\n",
       "      <td>ZNF72P</td>\n",
       "      <td>ZNF72BP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000232040</th>\n",
       "      <td>ZBED9</td>\n",
       "      <td>SCAND3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000215217</th>\n",
       "      <td>C5orf49</td>\n",
       "      <td>CFAP90</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000274225</th>\n",
       "      <td>LINC03038</td>\n",
       "      <td>HEPFAL</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000238259</th>\n",
       "      <td>PHF5GP</td>\n",
       "      <td>PHF5AP5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000181218</th>\n",
       "      <td>H2AW</td>\n",
       "      <td>H2AC25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000196890</th>\n",
       "      <td>H2BU1</td>\n",
       "      <td>H2BC26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000227946</th>\n",
       "      <td>INO80D-AS2</td>\n",
       "      <td>INO80D-AS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000237223</th>\n",
       "      <td>SULT1C2P1</td>\n",
       "      <td>SULT1C5P</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>121 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                       symb           0\n",
       "ensg                                   \n",
       "ENSG00000244646       XKRY2      XKRYP7\n",
       "ENSG00000184624      ZNF72P     ZNF72BP\n",
       "ENSG00000232040       ZBED9      SCAND3\n",
       "ENSG00000215217     C5orf49      CFAP90\n",
       "ENSG00000274225   LINC03038      HEPFAL\n",
       "...                     ...         ...\n",
       "ENSG00000238259      PHF5GP     PHF5AP5\n",
       "ENSG00000181218        H2AW      H2AC25\n",
       "ENSG00000196890       H2BU1      H2BC26\n",
       "ENSG00000227946  INO80D-AS2  INO80D-AS1\n",
       "ENSG00000237223   SULT1C2P1    SULT1C5P\n",
       "\n",
       "[121 rows x 2 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tempvar[tempvar.symb.notna() & tempvar[0].notna() & (tempvar.symb != tempvar[0])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "f5c980ff",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T17:55:28.724026Z",
     "start_time": "2022-12-27T17:55:28.548759Z"
    }
   },
   "outputs": [],
   "source": [
    "tempvar = sources[0]._data.merge(sources[1]._data,left_on='ensg',right_on='ensg',how='outer')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "071d110b",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T17:56:41.574236Z",
     "start_time": "2022-12-27T17:56:41.523730Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ensg</th>\n",
       "      <th>entr_x</th>\n",
       "      <th>symb_x</th>\n",
       "      <th>entr_y</th>\n",
       "      <th>symb_y</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>ENSG00000210151</td>\n",
       "      <td>113219467</td>\n",
       "      <td>MT-TS1</td>\n",
       "      <td>4574</td>\n",
       "      <td>MT-TS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>731</th>\n",
       "      <td>ENSG00000274917</td>\n",
       "      <td>124900510</td>\n",
       "      <td>RNA5-8SN5</td>\n",
       "      <td>100008587</td>\n",
       "      <td>RNA5-8SN5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>732</th>\n",
       "      <td>ENSG00000274917</td>\n",
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       "      <td>100008587</td>\n",
       "      <td>RNA5-8SN5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>733</th>\n",
       "      <td>ENSG00000274917</td>\n",
       "      <td>124907115</td>\n",
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       "      <td>100008587</td>\n",
       "      <td>RNA5-8SN5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>734</th>\n",
       "      <td>ENSG00000274917</td>\n",
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       "      <td>ENSG00000273768</td>\n",
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       "      <td>115409989</td>\n",
       "      <td>RNVU1-29</td>\n",
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       "      <th>75066</th>\n",
       "      <td>ENSG00000273768</td>\n",
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       "      <td>RNVU1-29</td>\n",
       "      <td>115409989</td>\n",
       "      <td>RNVU1-29</td>\n",
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       "    <tr>\n",
       "      <th>75067</th>\n",
       "      <td>ENSG00000273768</td>\n",
       "      <td>124905808</td>\n",
       "      <td>RNVU1-29</td>\n",
       "      <td>115409989</td>\n",
       "      <td>RNVU1-29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75068</th>\n",
       "      <td>ENSG00000273768</td>\n",
       "      <td>124905809</td>\n",
       "      <td>RNVU1-29</td>\n",
       "      <td>115409989</td>\n",
       "      <td>RNVU1-29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75070</th>\n",
       "      <td>ENSG00000274428</td>\n",
       "      <td>124904634</td>\n",
       "      <td>RNVU1-25</td>\n",
       "      <td>115409981</td>\n",
       "      <td>RNVU1-25</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3497 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  ensg     entr_x     symb_x     entr_y     symb_y\n",
       "16     ENSG00000210151  113219467     MT-TS1       4574     MT-TS1\n",
       "731    ENSG00000274917  124900510  RNA5-8SN5  100008587  RNA5-8SN5\n",
       "732    ENSG00000274917  124907114  RNA5-8SN5  100008587  RNA5-8SN5\n",
       "733    ENSG00000274917  124907115  RNA5-8SN5  100008587  RNA5-8SN5\n",
       "734    ENSG00000274917  124907116  RNA5-8SN5  100008587  RNA5-8SN5\n",
       "...                ...        ...        ...        ...        ...\n",
       "75065  ENSG00000273768  124905573   RNVU1-29  115409989   RNVU1-29\n",
       "75066  ENSG00000273768  124905574   RNVU1-29  115409989   RNVU1-29\n",
       "75067  ENSG00000273768  124905808   RNVU1-29  115409989   RNVU1-29\n",
       "75068  ENSG00000273768  124905809   RNVU1-29  115409989   RNVU1-29\n",
       "75070  ENSG00000274428  124904634   RNVU1-25  115409981   RNVU1-25\n",
       "\n",
       "[3497 rows x 5 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tempvar[tempvar.entr_x.notna() & tempvar.entr_y.notna() & (tempvar.entr_x != tempvar.entr_y)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "3c674fd5",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T18:24:14.484959Z",
     "start_time": "2022-12-27T18:24:14.298381Z"
    }
   },
   "outputs": [
    {
     "ename": "KeyError",
     "evalue": "0",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m idm \u001b[38;5;241m=\u001b[39m \u001b[43mm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mIDMapper\u001b[49m\u001b[43m(\u001b[49m\u001b[43msources\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      2\u001b[0m idm2 \u001b[38;5;241m=\u001b[39m m\u001b[38;5;241m.\u001b[39mIDMapper(sources2)\n",
      "File \u001b[0;32m~/Postdoc/Libs/biorosetta/main.py:83\u001b[0m, in \u001b[0;36mIDMapper.__init__\u001b[0;34m(self, sources)\u001b[0m\n\u001b[1;32m     81\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__init__\u001b[39m(\u001b[38;5;28mself\u001b[39m, sources):\n\u001b[1;32m     82\u001b[0m \t\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sources \u001b[38;5;241m=\u001b[39m {src\u001b[38;5;241m.\u001b[39msource_id:src \u001b[38;5;28;01mfor\u001b[39;00m src \u001b[38;5;129;01min\u001b[39;00m make_list(sources)}\n\u001b[0;32m---> 83\u001b[0m \t\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fill_value \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sources\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39m_fill_value\n",
      "\u001b[0;31mKeyError\u001b[0m: 0"
     ]
    }
   ],
   "source": [
    "idm = m.IDMapper(sources)\n",
    "idm2 = m.IDMapper(sources2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "94c8c766",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T18:23:59.242981Z",
     "start_time": "2022-12-27T18:23:59.213146Z"
    }
   },
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "IDMapper.convert() got an unexpected keyword argument 'report'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[28], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[43midm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mENSG00000210049\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mENSG00000278457\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mENSG00000233864\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mENSG00000244646\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mensg\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msymb\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43mreport\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m)\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28mprint\u001b[39m(idm2\u001b[38;5;241m.\u001b[39mconvert([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mENSG00000210049\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mENSG00000278457\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mENSG00000233864\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mENSG00000244646\u001b[39m\u001b[38;5;124m'\u001b[39m],\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mensg\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msymb\u001b[39m\u001b[38;5;124m'\u001b[39m))\n",
      "\u001b[0;31mTypeError\u001b[0m: IDMapper.convert() got an unexpected keyword argument 'report'"
     ]
    }
   ],
   "source": [
    "print(idm.convert(['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646'],'ensg','symb',report=True))\n",
    "print(idm2.convert(['ENSG00000210049','ENSG00000278457','ENSG00000233864','ENSG00000244646'],'ensg','symb'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "16902762",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T17:55:15.946583Z",
     "start_time": "2022-12-27T17:54:27.128965Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> \u001b[0;32m/Users/reema/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/generic.py\u001b[0m(9696)\u001b[0;36m_where\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m   9694 \u001b[0;31m            \u001b[0;31m# slice me out of the other\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   9695 \u001b[0;31m            \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m-> 9696 \u001b[0;31m                raise NotImplementedError(\n",
      "\u001b[0m\u001b[0;32m   9697 \u001b[0;31m                    \u001b[0;34m\"cannot align with a higher dimensional NDFrame\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   9698 \u001b[0;31m                )\n",
      "\u001b[0m\n",
      "ipdb> u\n",
      "> \u001b[0;32m/Users/reema/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/series.py\u001b[0m(1162)\u001b[0;36m__setitem__\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m   1160 \u001b[0;31m                \u001b[0;31m#  as series[mask] = other[mask]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   1161 \u001b[0;31m                \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m-> 1162 \u001b[0;31m                    \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_where\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m~\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minplace\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   1163 \u001b[0;31m                \u001b[0;32mexcept\u001b[0m \u001b[0mInvalidIndexError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   1164 \u001b[0;31m                    \u001b[0;31m# test_where_dups\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> u\n",
      "> \u001b[0;32m/Users/reema/Postdoc/Libs/biorosetta/main.py\u001b[0m(92)\u001b[0;36mconvert\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m     90 \u001b[0;31m                        \u001b[0;32mif\u001b[0m \u001b[0midx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msum\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[0;32m     91 \u001b[0;31m                                \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m---> 92 \u001b[0;31m                        \u001b[0mid_list_out\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_src_ids\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\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[0;32m     93 \u001b[0;31m                \u001b[0;32mreturn\u001b[0m \u001b[0mid_list_out\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtolist\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[0;32m     94 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> idx\n",
      "ensg\n",
      "ENSG00000210049    False\n",
      "ENSG00000211459    False\n",
      "ENSG00000233864     True\n",
      "Name: (ensembl,), dtype: bool\n",
      "ipdb> id_list_out\n",
      "ensg\n",
      "ENSG00000210049      MT-TF\n",
      "ENSG00000211459    MT-RNR1\n",
      "ENSG00000233864        N/A\n",
      "Name: (ensembl,), dtype: object\n",
      "ipdb> out_df.loc[idx,self._src_ids[1]]\n",
      "                   hgnc\n",
      "ensg                   \n",
      "ENSG00000233864  TTTY15\n",
      "ipdb> exit()\n"
     ]
    }
   ],
   "source": [
    "%debug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "b25498bd",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-27T17:11:08.895172Z",
     "start_time": "2022-12-27T16:59:14.587935Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> \u001b[0;32m/Users/reema/anaconda2/envs/biorosetta/lib/python3.10/site-packages/pandas/core/generic.py\u001b[0m(5902)\u001b[0;36m__getattr__\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m   5900 \u001b[0;31m        ):\n",
      "\u001b[0m\u001b[0;32m   5901 \u001b[0;31m            \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m-> 5902 \u001b[0;31m        \u001b[0;32mreturn\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattribute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   5903 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m   5904 \u001b[0;31m    \u001b[0;32mdef\u001b[0m \u001b[0m__setattr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> u\n",
      "> \u001b[0;32m/Users/reema/Postdoc/Libs/biorosetta/main.py\u001b[0m(79)\u001b[0;36mconvert\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m     77 \u001b[0;31m                        \u001b[0midx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mid_list_out\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_fill_value\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m     78 \u001b[0;31m                        \u001b[0mid_list_out\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mout_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_src_ids\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\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[0;32m---> 79 \u001b[0;31m                \u001b[0;32mreturn\u001b[0m \u001b[0mid_list_out\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtolist\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[0;32m     80 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\u001b[0;32m     81 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "ipdb> id_list_out\n",
      "                 biomart\n",
      "ensg                    \n",
      "ENSG00000210049    MT-TF\n",
      "ENSG00000211459  MT-RNR1\n",
      "ipdb> out_df[self._src_ids[0]]\n",
      "                 biomart\n",
      "ensg                    \n",
      "ENSG00000210049    MT-TF\n",
      "ENSG00000211459  MT-RNR1\n",
      "ipdb> self._src_ids[0]\n",
      "'biomart'\n",
      "ipdb> out_df['biomart']\n",
      "                 biomart\n",
      "ensg                    \n",
      "ENSG00000210049    MT-TF\n",
      "ENSG00000211459  MT-RNR1\n",
      "ipdb> type(out_df['biomart'])\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "ipdb> type(out_df['biomart'])\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "ipdb> out_df.biomart\n",
      "                 biomart\n",
      "ensg                    \n",
      "ENSG00000210049    MT-TF\n",
      "ENSG00000211459  MT-RNR1\n",
      "ipdb> type(out_df.biomart)\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "ipdb> pd.__version__\n",
      "'1.5.2'\n",
      "ipdb> out_df['biomart'].squeeze()\n",
      "ensg\n",
      "ENSG00000210049      MT-TF\n",
      "ENSG00000211459    MT-RNR1\n",
      "Name: (biomart,), dtype: object\n",
      "ipdb> type(out_df['biomart'].squeeze())\n",
      "<class 'pandas.core.series.Series'>\n",
      "ipdb> type(out_df['biomart'])\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "ipdb> exit\n"
     ]
    }
   ],
   "source": [
    "%debug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "80e59fff",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:14:11.603865Z",
     "start_time": "2022-12-26T18:14:11.591347Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ENSG00000210049', 'ENSG00000211459']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "src.convert(['MT-TF','MT-RNR1'],'symb','ensg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "f585223f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:25:49.311243Z",
     "start_time": "2022-12-26T18:25:49.292035Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ensg\n",
       "ENSG00000162543    UBXN10\n",
       "ENSG00000159023     EPB41\n",
       "sdasd                 N/A\n",
       "Name: symb, dtype: object"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "src.convert(['ENSG00000162543','ENSG00000159023','sdasd'],'ensg','symb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "5e7ffb6a",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:23:22.484975Z",
     "start_time": "2022-12-26T18:23:22.464205Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "entr\n",
       "127733    ENSG00000162543\n",
       "2035      ENSG00000159023\n",
       "dtype: object"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "src.convert(['127733','2035'],'entr','ensg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "cc7f791e",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:15:01.978596Z",
     "start_time": "2022-12-26T18:15:01.867845Z"
    }
   },
   "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>ensg</th>\n",
       "      <th>entr</th>\n",
       "      <th>symb</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000210049</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000211459</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-RNR1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000210077</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TV</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000210082</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-RNR2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000209082</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75108</th>\n",
       "      <td>ENSG00000162543</td>\n",
       "      <td>127733.0</td>\n",
       "      <td>UBXN10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75109</th>\n",
       "      <td>ENSG00000134686</td>\n",
       "      <td>1912.0</td>\n",
       "      <td>PHC2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75110</th>\n",
       "      <td>ENSG00000159023</td>\n",
       "      <td>2035.0</td>\n",
       "      <td>EPB41</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75111</th>\n",
       "      <td>ENSG00000198216</td>\n",
       "      <td>777.0</td>\n",
       "      <td>CACNA1E</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75112</th>\n",
       "      <td>ENSG00000159388</td>\n",
       "      <td>7832.0</td>\n",
       "      <td>BTG2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>75113 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  ensg      entr     symb\n",
       "0      ENSG00000210049       NaN    MT-TF\n",
       "1      ENSG00000211459       NaN  MT-RNR1\n",
       "2      ENSG00000210077       NaN    MT-TV\n",
       "3      ENSG00000210082       NaN  MT-RNR2\n",
       "4      ENSG00000209082       NaN   MT-TL1\n",
       "...                ...       ...      ...\n",
       "75108  ENSG00000162543  127733.0   UBXN10\n",
       "75109  ENSG00000134686    1912.0     PHC2\n",
       "75110  ENSG00000159023    2035.0    EPB41\n",
       "75111  ENSG00000198216     777.0  CACNA1E\n",
       "75112  ENSG00000159388    7832.0     BTG2\n",
       "\n",
       "[75113 rows x 3 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_table('data/biomart.tsv',sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "4f639e87",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:11:17.895087Z",
     "start_time": "2022-12-26T18:11:17.876452Z"
    }
   },
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'LocalSource' object has no attribute 'lookup'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[19], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msrc\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup\u001b[49m[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mensg\u001b[39m\u001b[38;5;124m'\u001b[39m][\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msymb\u001b[39m\u001b[38;5;124m'\u001b[39m]\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'LocalSource' object has no attribute 'lookup'"
     ]
    }
   ],
   "source": [
    "src.lookup['ensg']['symb']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "7d2864c9",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:52:54.338652Z",
     "start_time": "2022-12-26T17:52:52.268495Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "data/biomart.tsv: 1.84MiB [00:01, 1.21MiB/s]\n"
     ]
    }
   ],
   "source": [
    "utils.download_biomart()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "538167d1",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:52:55.819072Z",
     "start_time": "2022-12-26T17:52:55.729687Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\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>ensg</th>\n",
       "      <th>entr</th>\n",
       "      <th>symb</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000210049</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000211459</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-RNR1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000210077</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TV</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000210082</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-RNR2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000209082</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75108</th>\n",
       "      <td>ENSG00000162543</td>\n",
       "      <td>127733.0</td>\n",
       "      <td>UBXN10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75109</th>\n",
       "      <td>ENSG00000134686</td>\n",
       "      <td>1912.0</td>\n",
       "      <td>PHC2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75110</th>\n",
       "      <td>ENSG00000159023</td>\n",
       "      <td>2035.0</td>\n",
       "      <td>EPB41</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75111</th>\n",
       "      <td>ENSG00000198216</td>\n",
       "      <td>777.0</td>\n",
       "      <td>CACNA1E</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75112</th>\n",
       "      <td>ENSG00000159388</td>\n",
       "      <td>7832.0</td>\n",
       "      <td>BTG2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>75113 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  ensg      entr     symb\n",
       "0      ENSG00000210049       NaN    MT-TF\n",
       "1      ENSG00000211459       NaN  MT-RNR1\n",
       "2      ENSG00000210077       NaN    MT-TV\n",
       "3      ENSG00000210082       NaN  MT-RNR2\n",
       "4      ENSG00000209082       NaN   MT-TL1\n",
       "...                ...       ...      ...\n",
       "75108  ENSG00000162543  127733.0   UBXN10\n",
       "75109  ENSG00000134686    1912.0     PHC2\n",
       "75110  ENSG00000159023    2035.0    EPB41\n",
       "75111  ENSG00000198216     777.0  CACNA1E\n",
       "75112  ENSG00000159388    7832.0     BTG2\n",
       "\n",
       "[75113 rows x 3 columns]"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_table('data/biomart.tsv',sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "d47d3c75",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:49:04.520820Z",
     "start_time": "2022-12-26T17:49:04.377139Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ensg</th>\n",
       "      <th>entr</th>\n",
       "      <th>symb</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000210049</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000211459</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-RNR1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000210077</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TV</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000210082</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-RNR2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000209082</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MT-TL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>75108</th>\n",
       "      <td>ENSG00000162543</td>\n",
       "      <td>127733</td>\n",
       "      <td>UBXN10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75109</th>\n",
       "      <td>ENSG00000134686</td>\n",
       "      <td>1912</td>\n",
       "      <td>PHC2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75110</th>\n",
       "      <td>ENSG00000159023</td>\n",
       "      <td>2035</td>\n",
       "      <td>EPB41</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75111</th>\n",
       "      <td>ENSG00000198216</td>\n",
       "      <td>777</td>\n",
       "      <td>CACNA1E</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75112</th>\n",
       "      <td>ENSG00000159388</td>\n",
       "      <td>7832</td>\n",
       "      <td>BTG2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>75113 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  ensg    entr     symb\n",
       "0      ENSG00000210049     NaN    MT-TF\n",
       "1      ENSG00000211459     NaN  MT-RNR1\n",
       "2      ENSG00000210077     NaN    MT-TV\n",
       "3      ENSG00000210082     NaN  MT-RNR2\n",
       "4      ENSG00000209082     NaN   MT-TL1\n",
       "...                ...     ...      ...\n",
       "75108  ENSG00000162543  127733   UBXN10\n",
       "75109  ENSG00000134686    1912     PHC2\n",
       "75110  ENSG00000159023    2035    EPB41\n",
       "75111  ENSG00000198216     777  CACNA1E\n",
       "75112  ENSG00000159388    7832     BTG2\n",
       "\n",
       "[75113 rows x 3 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_table('data/biomart.tsv', header=None, names=['ensg', 'symb', 'entr'], dtype={'entr': 'str'})[['ensg','entr','symb']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "447d6b13",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:16:31.274456Z",
     "start_time": "2022-12-26T17:16:26.710129Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "data/biomart.tsv: 1.84MiB [00:03, 491kiB/s] \n"
     ]
    }
   ],
   "source": [
    "src.download_biomart()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "3eb82037",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:44:17.499536Z",
     "start_time": "2022-12-26T17:44:17.453227Z"
    }
   },
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'LocalSource' object has no attribute '_data'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[15], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msrc\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minit\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/Postdoc/Libs/biorosetta/main.py:27\u001b[0m, in \u001b[0;36mLocalSource.init\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     26\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21minit\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m---> 27\u001b[0m \tdata \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_data\u001b[49m\n\u001b[1;32m     28\u001b[0m \tdata \u001b[38;5;241m=\u001b[39m data[\u001b[38;5;241m~\u001b[39mdata\u001b[38;5;241m.\u001b[39mduplicated()]\n\u001b[1;32m     30\u001b[0m \t\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mlookup \u001b[38;5;241m=\u001b[39m {}\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'LocalSource' object has no attribute '_data'"
     ]
    }
   ],
   "source": [
    "src.init()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "1d4dc3b4",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:27:05.919105Z",
     "start_time": "2022-12-26T17:27:05.812637Z"
    }
   },
   "outputs": [],
   "source": [
    "biomart = pd.read_table('data/biomart.tsv',header=None,names=['ensg','symb','entr'], dtype={'entr':'str'})[['ensg','symb','entr']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "4bba12af",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:30:49.811487Z",
     "start_time": "2022-12-26T17:30:49.803617Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'aaa'"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "min(['ciao','fdsfdsf','aaa'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "id": "96c3f2bf",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:27:42.374858Z",
     "start_time": "2022-12-23T18:27:42.367744Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "284514"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(biomart)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "id": "d1183fb4",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:27:43.302558Z",
     "start_time": "2022-12-23T18:27:43.131340Z"
    }
   },
   "outputs": [],
   "source": [
    "biomart = biomart[~biomart.duplicated()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "id": "f2ff5fbb",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:44:30.125350Z",
     "start_time": "2022-12-23T18:44:30.119699Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(35733, 3)"
      ]
     },
     "execution_count": 107,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pruned.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 118,
   "id": "e761ce4c",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:47:16.531622Z",
     "start_time": "2022-12-23T18:47:16.525346Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5821"
      ]
     },
     "execution_count": 118,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(~id_in_unq).sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 119,
   "id": "23bba12e",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:47:25.628929Z",
     "start_time": "2022-12-23T18:47:25.623031Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "29912"
      ]
     },
     "execution_count": 119,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_in_unq.sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 174,
   "id": "2c60ddeb",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T16:25:40.863338Z",
     "start_time": "2022-12-26T16:25:40.859548Z"
    }
   },
   "outputs": [],
   "source": [
    "def selection(id_in,id_out_list):\n",
    "    return min(map(int,id_out_list))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "fb7e50cd",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:09:19.529751Z",
     "start_time": "2022-12-26T18:09:19.516242Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ensg\n",
       "ENSG00000210049      MT-TF\n",
       "ENSG00000211459    MT-RNR1\n",
       "ENSG00000210077      MT-TV\n",
       "ENSG00000210082    MT-RNR2\n",
       "ENSG00000209082     MT-TL1\n",
       "                    ...   \n",
       "ENSG00000162543     UBXN10\n",
       "ENSG00000134686       PHC2\n",
       "ENSG00000159023      EPB41\n",
       "ENSG00000198216    CACNA1E\n",
       "ENSG00000159388       BTG2\n",
       "Name: symb, Length: 46761, dtype: object"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "unq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "4446225d",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:10:06.423655Z",
     "start_time": "2022-12-26T18:10:06.247624Z"
    }
   },
   "outputs": [],
   "source": [
    "biomart = pd.read_table('data/biomart.tsv',sep='\\t', dtype={'entr': 'str'})\n",
    "\n",
    "id_in = 'ensg'\n",
    "id_out = 'symb'\n",
    "\n",
    "pruned = biomart[biomart[id_in].notna() & biomart[id_out].notna()]\n",
    "\n",
    "pruned = pruned[~pruned.duplicated(subset=[id_in,id_out])]\n",
    "\n",
    "id_in_unq = ~pruned.duplicated(subset=[id_in], keep=False)\n",
    "\n",
    "unq = pruned.loc[id_in_unq].set_index(id_in)[id_out]\n",
    "\n",
    "if (~id_in_unq).sum() > 0:\n",
    "    nonunq = pruned.loc[~id_in_unq,[id_in,id_out]].groupby(id_in).apply(lambda x: selection(x.name, x[id_out]))\n",
    "    final = pd.concat([unq,nonunq])\n",
    "else:\n",
    "    final = unq\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "fd3d5404",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T18:10:12.693358Z",
     "start_time": "2022-12-26T18:10:12.677200Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ensg\n",
       "ENSG00000210049      MT-TF\n",
       "ENSG00000211459    MT-RNR1\n",
       "ENSG00000210077      MT-TV\n",
       "ENSG00000210082    MT-RNR2\n",
       "ENSG00000209082     MT-TL1\n",
       "                    ...   \n",
       "ENSG00000162543     UBXN10\n",
       "ENSG00000134686       PHC2\n",
       "ENSG00000159023      EPB41\n",
       "ENSG00000198216    CACNA1E\n",
       "ENSG00000159388       BTG2\n",
       "Name: symb, Length: 46761, dtype: object"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 194,
   "id": "cf1c0f64",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T17:03:44.885835Z",
     "start_time": "2022-12-26T17:03:44.870849Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(29912,)"
      ]
     },
     "execution_count": 194,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pruned.ensg.unique().shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 140,
   "id": "ec344ac0",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T16:11:44.635056Z",
     "start_time": "2022-12-26T16:11:29.613949Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.84 s ± 99.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit pruned.groupby('ensg').apply(lambda x: '|'.join(x.entr))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 145,
   "id": "d76f502c",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T16:14:43.800356Z",
     "start_time": "2022-12-26T16:14:39.874333Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "48.8 ms ± 6.33 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
     ]
    }
   ],
   "source": [
    "%timeit nonunq.groupby('ensg').apply(lambda x: '|'.join(x.entr))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 144,
   "id": "611055d8",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T16:13:46.579243Z",
     "start_time": "2022-12-26T16:13:46.514978Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ensg\n",
       "ENSG00000004866                                           7982|93655\n",
       "ENSG00000063587                                      10838|105373378\n",
       "ENSG00000065615                                      51167|123956252\n",
       "ENSG00000076554                                       7163|124188259\n",
       "ENSG00000079974                                          11158|11159\n",
       "ENSG00000088298                                      55741|111089941\n",
       "ENSG00000090857                                      55066|124907803\n",
       "ENSG00000099977                                       1652|100037417\n",
       "ENSG00000101883                                     158800|104797536\n",
       "ENSG00000105793                                      85865|101927446\n",
       "ENSG00000105889                                        256227|401312\n",
       "ENSG00000108379                                       7473|101929777\n",
       "ENSG00000109927                                       7007|116804918\n",
       "ENSG00000111215                                           5554|11272\n",
       "ENSG00000111671                                      84727|105369632\n",
       "ENSG00000111850                                          57150|63914\n",
       "ENSG00000112541                                          10846|90632\n",
       "ENSG00000112679                                      56940|124907782\n",
       "ENSG00000114374                                           8287|64595\n",
       "ENSG00000115239                                      51130|100302652\n",
       "ENSG00000120088                                       1394|104909134\n",
       "ENSG00000120341                                      89866|111240474\n",
       "ENSG00000120709                                      51307|100128966\n",
       "ENSG00000124343                                       7499|100132596\n",
       "ENSG00000124713                                      27232|107080644\n",
       "ENSG00000126861                                       4974|101927057\n",
       "ENSG00000128383                                     200315|100913187\n",
       "ENSG00000132207                               79008|548593|124907837\n",
       "ENSG00000134986                                       9315|124906525\n",
       "ENSG00000137843                                      56924|106821730\n",
       "ENSG00000137962                                       9411|105378858\n",
       "ENSG00000140839                                     497190|124907805\n",
       "ENSG00000143384                                          4170|574406\n",
       "ENSG00000143702                                          9859|645455\n",
       "ENSG00000144455                                     285362|100130207\n",
       "ENSG00000145002                                     653333|124900625\n",
       "ENSG00000145736                                          2966|728340\n",
       "ENSG00000145979                                      51256|107080638\n",
       "ENSG00000146112                                     170954|107987457\n",
       "ENSG00000149557                                       9638|105369550\n",
       "ENSG00000151067                                        775|100874369\n",
       "ENSG00000152082                                         80097|653784\n",
       "ENSG00000152926                                      51351|109504726\n",
       "ENSG00000156273                                        571|100379661\n",
       "ENSG00000157335                    283971|497190|124907799|124907806\n",
       "ENSG00000157429                                       7567|124903710\n",
       "ENSG00000158169                                       2176|105376156\n",
       "ENSG00000158301                                     114928|100528062\n",
       "ENSG00000158406                                          8365|554313\n",
       "ENSG00000158747                                       4681|100532736\n",
       "                                         ...                        \n",
       "ENSG00000285181                             1673|100289462|124906748\n",
       "ENSG00000285285    100169753|124905422|124905424|124905425|124905...\n",
       "ENSG00000285286                                  100131980|124900627\n",
       "ENSG00000285356                                     503618|124906746\n",
       "ENSG00000285376                                     414325|124906744\n",
       "ENSG00000285411                                     504180|124906747\n",
       "ENSG00000285432                              245910|503614|124906743\n",
       "ENSG00000285433                             1673|100289462|124906748\n",
       "ENSG00000285479                                        775|100874369\n",
       "ENSG00000285607    441327|645651|124906721|124906722|124906751|12...\n",
       "ENSG00000285617                                     245909|124906749\n",
       "ENSG00000285765                                     645572|124906757\n",
       "ENSG00000285795                                     645572|124906757\n",
       "ENSG00000285832                                        441317|441327\n",
       "ENSG00000285950                           441328|124906735|124906766\n",
       "ENSG00000285962    441327|645651|124906721|124906722|124906751|12...\n",
       "ENSG00000285975                                        441317|441327\n",
       "ENSG00000286014                           641776|105180390|105180391\n",
       "ENSG00000286038                           641776|105180390|105180391\n",
       "ENSG00000286137                           641776|105180390|105180391\n",
       "ENSG00000286190                                     728392|124900388\n",
       "ENSG00000287664    102723851|102724956|105371848|105371853|124900636\n",
       "ENSG00000288147                                     389831|124900580\n",
       "ENSG00000288164                                  102723573|102724737\n",
       "ENSG00000288184                                  124907096|124907358\n",
       "ENSG00000288205                        124904108|124904706|124906683\n",
       "ENSG00000288214                 283767|124900581|124905482|124907501\n",
       "ENSG00000288249                                  124907096|124907358\n",
       "ENSG00000288273                                        255313|728062\n",
       "ENSG00000288309                                      10407|124906741\n",
       "ENSG00000288326    106632260|124900510|124907114|124907115|124907...\n",
       "ENSG00000288357                                           3810|57292\n",
       "ENSG00000288387    109910381|124900510|124907114|124907115|124907...\n",
       "ENSG00000288487                                          3808|553128\n",
       "ENSG00000288811              105372935|105372942|105377182|105379548\n",
       "ENSG00000288905                                     645166|107985200\n",
       "ENSG00000289007                                  101928092|124908546\n",
       "ENSG00000290355                                     727856|100287029\n",
       "ENSG00000290614                                        150527|646743\n",
       "ENSG00000290633                           727856|100287596|100288486\n",
       "ENSG00000290751                                          6953|401285\n",
       "ENSG00000290824                           727856|100287596|100288486\n",
       "ENSG00000290825           84771|727856|100287102|100287596|102725121\n",
       "ENSG00000291016                                         84559|401634\n",
       "ENSG00000291031                                     286554|105377223\n",
       "ENSG00000291050                                  100132288|100233156\n",
       "ENSG00000291150                                     645166|107985911\n",
       "ENSG00000291153                                      64940|101929736\n",
       "ENSG00000291154                                            5380|5382\n",
       "ENSG00000291158                                         57234|388692\n",
       "Length: 619, dtype: object"
      ]
     },
     "execution_count": 144,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nonunq.groupby('ensg').apply(lambda x: '|'.join(x.entr))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 137,
   "id": "b9138671",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T15:50:07.118114Z",
     "start_time": "2022-12-26T15:50:07.024357Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ensg\n",
       "ENSG00000004866                                              [93655]\n",
       "ENSG00000063587                                          [105373378]\n",
       "ENSG00000065615                                          [123956252]\n",
       "ENSG00000076554                                          [124188259]\n",
       "ENSG00000079974                                              [11159]\n",
       "ENSG00000088298                                          [111089941]\n",
       "ENSG00000090857                                          [124907803]\n",
       "ENSG00000099977                                          [100037417]\n",
       "ENSG00000101883                                          [104797536]\n",
       "ENSG00000105793                                          [101927446]\n",
       "ENSG00000105889                                             [401312]\n",
       "ENSG00000108379                                          [101929777]\n",
       "ENSG00000109927                                          [116804918]\n",
       "ENSG00000111215                                              [11272]\n",
       "ENSG00000111671                                          [105369632]\n",
       "ENSG00000111850                                              [63914]\n",
       "ENSG00000112541                                              [90632]\n",
       "ENSG00000112679                                          [124907782]\n",
       "ENSG00000114374                                              [64595]\n",
       "ENSG00000115239                                          [100302652]\n",
       "ENSG00000120088                                          [104909134]\n",
       "ENSG00000120341                                          [111240474]\n",
       "ENSG00000120709                                          [100128966]\n",
       "ENSG00000124343                                          [100132596]\n",
       "ENSG00000124713                                          [107080644]\n",
       "ENSG00000126861                                          [101927057]\n",
       "ENSG00000128383                                          [100913187]\n",
       "ENSG00000132207                                  [548593, 124907837]\n",
       "ENSG00000134986                                          [124906525]\n",
       "ENSG00000137843                                          [106821730]\n",
       "ENSG00000137962                                          [105378858]\n",
       "ENSG00000140839                                          [124907805]\n",
       "ENSG00000143384                                             [574406]\n",
       "ENSG00000143702                                             [645455]\n",
       "ENSG00000144455                                          [100130207]\n",
       "ENSG00000145002                                          [124900625]\n",
       "ENSG00000145736                                             [728340]\n",
       "ENSG00000145979                                          [107080638]\n",
       "ENSG00000146112                                          [107987457]\n",
       "ENSG00000149557                                          [105369550]\n",
       "ENSG00000151067                                          [100874369]\n",
       "ENSG00000152082                                             [653784]\n",
       "ENSG00000152926                                          [109504726]\n",
       "ENSG00000156273                                          [100379661]\n",
       "ENSG00000157335                       [497190, 124907799, 124907806]\n",
       "ENSG00000157429                                          [124903710]\n",
       "ENSG00000158169                                          [105376156]\n",
       "ENSG00000158301                                          [100528062]\n",
       "ENSG00000158406                                             [554313]\n",
       "ENSG00000158747                                          [100532736]\n",
       "                                         ...                        \n",
       "ENSG00000285181                               [100289462, 124906748]\n",
       "ENSG00000285285    [124905422, 124905424, 124905425, 124905426, 1...\n",
       "ENSG00000285286                                          [124900627]\n",
       "ENSG00000285356                                          [124906746]\n",
       "ENSG00000285376                                          [124906744]\n",
       "ENSG00000285411                                          [124906747]\n",
       "ENSG00000285432                                  [503614, 124906743]\n",
       "ENSG00000285433                               [100289462, 124906748]\n",
       "ENSG00000285479                                          [100874369]\n",
       "ENSG00000285607    [645651, 124906721, 124906722, 124906751, 1249...\n",
       "ENSG00000285617                                          [124906749]\n",
       "ENSG00000285765                                          [124906757]\n",
       "ENSG00000285795                                          [124906757]\n",
       "ENSG00000285832                                             [441327]\n",
       "ENSG00000285950                               [124906735, 124906766]\n",
       "ENSG00000285962    [645651, 124906721, 124906722, 124906751, 1249...\n",
       "ENSG00000285975                                             [441327]\n",
       "ENSG00000286014                               [105180390, 105180391]\n",
       "ENSG00000286038                               [105180390, 105180391]\n",
       "ENSG00000286137                               [105180390, 105180391]\n",
       "ENSG00000286190                                          [124900388]\n",
       "ENSG00000287664         [102724956, 105371848, 105371853, 124900636]\n",
       "ENSG00000288147                                          [124900580]\n",
       "ENSG00000288164                                          [102724737]\n",
       "ENSG00000288184                                          [124907358]\n",
       "ENSG00000288205                               [124904706, 124906683]\n",
       "ENSG00000288214                    [124900581, 124905482, 124907501]\n",
       "ENSG00000288249                                          [124907358]\n",
       "ENSG00000288273                                             [728062]\n",
       "ENSG00000288309                                          [124906741]\n",
       "ENSG00000288326    [124900510, 124907114, 124907115, 124907116, 1...\n",
       "ENSG00000288357                                              [57292]\n",
       "ENSG00000288387    [124900510, 124907114, 124907115, 124907116, 1...\n",
       "ENSG00000288487                                             [553128]\n",
       "ENSG00000288811                    [105372942, 105377182, 105379548]\n",
       "ENSG00000288905                                          [107985200]\n",
       "ENSG00000289007                                          [124908546]\n",
       "ENSG00000290355                                          [100287029]\n",
       "ENSG00000290614                                             [646743]\n",
       "ENSG00000290633                               [100287596, 100288486]\n",
       "ENSG00000290751                                             [401285]\n",
       "ENSG00000290824                               [100287596, 100288486]\n",
       "ENSG00000290825            [727856, 100287102, 100287596, 102725121]\n",
       "ENSG00000291016                                             [401634]\n",
       "ENSG00000291031                                          [105377223]\n",
       "ENSG00000291050                                          [100233156]\n",
       "ENSG00000291150                                          [107985911]\n",
       "ENSG00000291153                                          [101929736]\n",
       "ENSG00000291154                                               [5382]\n",
       "ENSG00000291158                                             [388692]\n",
       "Length: 619, dtype: object"
      ]
     },
     "execution_count": 137,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nonunq.groupby('ensg').apply(lambda x: '|'.join(x.entr)).str.split('|')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 127,
   "id": "927d5a29",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T15:39:33.722014Z",
     "start_time": "2022-12-26T15:39:33.671877Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "124900568    41\n",
       "124906463    23\n",
       "124906457    23\n",
       "124905410    23\n",
       "124905411    23\n",
       "124906452    23\n",
       "124906453    23\n",
       "124906454    23\n",
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       "124905409    23\n",
       "124906461    23\n",
       "124905830    21\n",
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       "124905798    21\n",
       "124905797    21\n",
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       "124905833    21\n",
       "124905834    21\n",
       "124905836    21\n",
       "124905804    21\n",
       "124905837    21\n",
       "124905838    21\n",
       "124905839    21\n",
       "124905840    21\n",
       "124905841    21\n",
       "124905842    21\n",
       "124905843    21\n",
       "124905844    21\n",
       "124905845    21\n",
       "124905803    21\n",
       "124905805    21\n",
       "124905829    21\n",
       "124905819    21\n",
       "124905828    21\n",
       "124905827    21\n",
       "124905826    21\n",
       "124905825    21\n",
       "124905824    21\n",
       "124905823    21\n",
       "             ..\n",
       "728689        1\n",
       "105372942     1\n",
       "105377182     1\n",
       "105379548     1\n",
       "100529261     1\n",
       "124907803     1\n",
       "124907389     1\n",
       "105369550     1\n",
       "101928198     1\n",
       "105378858     1\n",
       "124902155     1\n",
       "107986281     1\n",
       "124905557     1\n",
       "124188259     1\n",
       "100534012     1\n",
       "107986583     1\n",
       "101930112     1\n",
       "100528062     1\n",
       "548593        1\n",
       "124907841     1\n",
       "124907523     1\n",
       "124906525     1\n",
       "101929800     1\n",
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       "100271849     1\n",
       "105375707     1\n",
       "100528032     1\n",
       "107983961     1\n",
       "102724956     1\n",
       "105371848     1\n",
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       "124900636     1\n",
       "105371828     1\n",
       "105376382     1\n",
       "103157000     1\n",
       "654483        1\n",
       "11159         1\n",
       "107080638     1\n",
       "124908528     1\n",
       "107080644     1\n",
       "653166        1\n",
       "124908013     1\n",
       "124908015     1\n",
       "124908041     1\n",
       "100132596     1\n",
       "728656        1\n",
       "105374836     1\n",
       "100302652     1\n",
       "100158262     1\n",
       "100532736     1\n",
       "Name: entr, Length: 764, dtype: int64"
      ]
     },
     "execution_count": 127,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nonunq.entr.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 126,
   "id": "66db6ac2",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-26T15:39:19.431142Z",
     "start_time": "2022-12-26T15:39:18.127115Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "entr\n",
       "100008586                                      ENSG00000236362\n",
       "100037417                      ENSG00000275003|ENSG00000099977\n",
       "100101629                                      ENSG00000189064\n",
       "100128966                                      ENSG00000120709\n",
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       "100133251      ENSG00000274540|ENSG00000284870|ENSG00000255251\n",
       "100158262                                      ENSG00000254911\n",
       "100169763                      ENSG00000285168|ENSG00000199337\n",
       "100233156                                      ENSG00000291050\n",
       "100271849                                      ENSG00000213999\n",
       "100271927                                      ENSG00000170667\n",
       "100287029                                      ENSG00000290355\n",
       "100287083                                      ENSG00000215378\n",
       "100287102                                      ENSG00000290825\n",
       "100287596      ENSG00000290633|ENSG00000290824|ENSG00000290825\n",
       "100288486                      ENSG00000290633|ENSG00000290824\n",
       "100289137                                      ENSG00000180071\n",
       "100289462    ENSG00000275444|ENSG00000285433|ENSG0000028518...\n",
       "100302652                                      ENSG00000115239\n",
       "100379661                                      ENSG00000156273\n",
       "100499467                                      ENSG00000227036\n",
       "100505385                                      ENSG00000283154\n",
       "100505555                                      ENSG00000196605\n",
       "100506084    ENSG00000276276|ENSG00000275748|ENSG0000018582...\n",
       "100506403                                      ENSG00000159216\n",
       "100507257                                      ENSG00000223403\n",
       "100507547    ENSG00000238056|ENSG00000229071|ENSG0000022514...\n",
       "100507608                                      ENSG00000267635\n",
       "100526832                                      ENSG00000213160\n",
       "100527964                                      ENSG00000230124\n",
       "100528032                                      ENSG00000213809\n",
       "100528062                                      ENSG00000158301\n",
       "100529215                                      ENSG00000188629\n",
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       "100533183                                      ENSG00000178882\n",
       "100534012                                      ENSG00000163156\n",
       "100859930                                      ENSG00000278970\n",
       "100874074                                      ENSG00000176124\n",
       "100874185                                      ENSG00000258537\n",
       "100874369                      ENSG00000285479|ENSG00000151067\n",
       "100913187                      ENSG00000262156|ENSG00000128383\n",
       "100996709    ENSG00000276276|ENSG00000275748|ENSG0000018582...\n",
       "100996746                                      ENSG00000275976\n",
       "101060321      ENSG00000278632|ENSG00000274939|ENSG00000274808\n",
       "101060376                      ENSG00000276349|ENSG00000274512\n",
       "101927055                                      ENSG00000237298\n",
       "101927057                                      ENSG00000126861\n",
       "                                   ...                        \n",
       "5382                                           ENSG00000291154\n",
       "548593                                         ENSG00000132207\n",
       "548596                         ENSG00000237289|ENSG00000223572\n",
       "553128                                         ENSG00000288487\n",
       "554313       ENSG00000278637|ENSG00000277157|ENSG0000027512...\n",
       "57292                                          ENSG00000288357\n",
       "574406                                         ENSG00000143384\n",
       "63914                                          ENSG00000111850\n",
       "642799       ENSG00000278308|ENSG00000281994|ENSG0000022471...\n",
       "643909       ENSG00000262461|ENSG00000275976|ENSG0000018664...\n",
       "645037                                         ENSG00000189064\n",
       "645073                                         ENSG00000215269\n",
       "645202                         ENSG00000282475|ENSG00000237850\n",
       "645359       ENSG00000276299|ENSG00000282566|ENSG0000028334...\n",
       "645402                         ENSG00000284781|ENSG00000236125\n",
       "645455                         ENSG00000276725|ENSG00000143702\n",
       "645651                         ENSG00000285962|ENSG00000285607\n",
       "64595                                          ENSG00000114374\n",
       "645961                                         ENSG00000177910\n",
       "646743                                         ENSG00000290614\n",
       "646982                                         ENSG00000215483\n",
       "647042                         ENSG00000274166|ENSG00000278662\n",
       "653125                         ENSG00000284076|ENSG00000261247\n",
       "653166                                         ENSG00000262628\n",
       "653247         ENSG00000275517|ENSG00000282673|ENSG00000251655\n",
       "653499       ENSG00000282902|ENSG00000283082|ENSG0000017893...\n",
       "653550                                         ENSG00000183632\n",
       "653784                                         ENSG00000152082\n",
       "654483                                         ENSG00000169627\n",
       "6607           ENSG00000273772|ENSG00000277773|ENSG00000205571\n",
       "677885                                         ENSG00000239149\n",
       "727856                                         ENSG00000290825\n",
       "727866                         ENSG00000268350|ENSG00000179304\n",
       "728047                         ENSG00000282773|ENSG00000178115\n",
       "728062                         ENSG00000288273|ENSG00000226023\n",
       "728340         ENSG00000276910|ENSG00000275045|ENSG00000145736\n",
       "728492         ENSG00000277429|ENSG00000278839|ENSG00000205572\n",
       "728524                                         ENSG00000273520\n",
       "728656                                         ENSG00000269502\n",
       "728689                                         ENSG00000184110\n",
       "728724                                         ENSG00000229140\n",
       "729355                                         ENSG00000261509\n",
       "729408                                         ENSG00000189064\n",
       "729447                                         ENSG00000189064\n",
       "729759                                         ENSG00000284733\n",
       "729873                                         ENSG00000274611\n",
       "81399                                          ENSG00000230178\n",
       "84773                                          ENSG00000187954\n",
       "90632                                          ENSG00000112541\n",
       "93655                                          ENSG00000004866\n",
       "Length: 764, dtype: object"
      ]
     },
     "execution_count": 126,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nonunq.groupby('entr').apply(lambda x: '|'.join(x.ensg))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e03405c5",
   "metadata": {},
   "outputs": [],
   "source": [
    "nonunq.groupby('entr').apply(lambda x: '|'.join(x.ensg))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 122,
   "id": "86296cb3",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-24T08:16:35.325355Z",
     "start_time": "2022-12-24T08:16:35.299412Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "ENSG00000288326    210\n",
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       "                  ... \n",
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       "ENSG00000276297      1\n",
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       "Name: ensg, Length: 619, dtype: int64"
      ]
     },
     "execution_count": 122,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nonunq.ensg.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 93,
   "id": "37972a6d",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:38:52.168704Z",
     "start_time": "2022-12-23T18:38:52.117771Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "619"
      ]
     },
     "execution_count": 93,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(pruned[~pruned.duplicated(subset=[idclass_in,idclass_out])].ensg.value_counts()>1).sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 96,
   "id": "1713a415",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:39:18.613397Z",
     "start_time": "2022-12-23T18:39:18.608278Z"
    }
   },
   "outputs": [],
   "source": [
    "pd.options.display.max_rows = 100\n",
    "pd.options.display.min_rows = 100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "id": "12acf3c4",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:39:14.337115Z",
     "start_time": "2022-12-23T18:39:14.306575Z"
    }
   },
   "outputs": [
    {
     "data": {
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      ],
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       "                  ensg       symb       entr\n",
       "25354  ENSG00000275215  RNA5-8SN3  109910381\n",
       "25355  ENSG00000275215  RNA5-8SN3  124900510\n",
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       "...                ...        ...        ...\n",
       "25560  ENSG00000275215  RNA5-8SN3  124908523\n",
       "25561  ENSG00000275215  RNA5-8SN3  124908524\n",
       "25562  ENSG00000275215  RNA5-8SN3  124908525\n",
       "25563  ENSG00000275215  RNA5-8SN3  124908526\n",
       "25564  ENSG00000275215  RNA5-8SN3  124908527\n",
       "\n",
       "[211 rows x 3 columns]"
      ]
     },
     "execution_count": 95,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pruned[~pruned.duplicated(subset=[idclass_in,idclass_out])].query('ensg == \"ENSG00000275215\"')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "id": "108e84b4",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:28:15.852611Z",
     "start_time": "2022-12-23T18:28:15.825571Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2133"
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(biomart.entr.value_counts()>1).sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "id": "ec67a38d",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:33:28.131357Z",
     "start_time": "2022-12-23T18:33:28.000480Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ENSG00000275215    211\n",
       "ENSG00000278233    211\n",
       "ENSG00000278189    211\n",
       "ENSG00000288387    211\n",
       "ENSG00000276700    211\n",
       "                  ... \n",
       "ENSG00000212221      1\n",
       "ENSG00000279004      1\n",
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       "ENSG00000277732      1\n",
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     },
     "execution_count": 88,
     "metadata": {},
     "output_type": "execute_result"
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   "source": [
    "biomart.ensg.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "id": "e0c7c497",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:33:38.772942Z",
     "start_time": "2022-12-23T18:33:38.752210Z"
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   "outputs": [
    {
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      ],
      "text/plain": [
       "                  ensg       symb       entr\n",
       "25354  ENSG00000275215  RNA5-8SN3  109910381\n",
       "25355  ENSG00000275215  RNA5-8SN3  124900510\n",
       "25356  ENSG00000275215  RNA5-8SN3  124907114\n",
       "25357  ENSG00000275215  RNA5-8SN3  124907115\n",
       "25358  ENSG00000275215  RNA5-8SN3  124907116\n",
       "...                ...        ...        ...\n",
       "25560  ENSG00000275215  RNA5-8SN3  124908523\n",
       "25561  ENSG00000275215  RNA5-8SN3  124908524\n",
       "25562  ENSG00000275215  RNA5-8SN3  124908525\n",
       "25563  ENSG00000275215  RNA5-8SN3  124908526\n",
       "25564  ENSG00000275215  RNA5-8SN3  124908527\n",
       "\n",
       "[211 rows x 3 columns]"
      ]
     },
     "execution_count": 89,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "biomart[biomart.ensg == 'ENSG00000275215']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "id": "6069c269",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:32:36.712716Z",
     "start_time": "2022-12-23T18:32:36.686776Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3812         43\n",
       "115653       42\n",
       "79166        41\n",
       "3805         41\n",
       "124900568    41\n",
       "             ..\n",
       "400961        1\n",
       "122740        1\n",
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       "100507210     1\n",
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      ]
     },
     "execution_count": 87,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pruned[idclass_out].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e6a5fe00",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "6f0d1edc",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:13:43.034805Z",
     "start_time": "2022-12-23T18:13:43.004562Z"
    }
   },
   "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>ensg</th>\n",
       "      <th>symb</th>\n",
       "      <th>entr</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000210049</td>\n",
       "      <td>MT-TF</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000211459</td>\n",
       "      <td>MT-RNR1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000210077</td>\n",
       "      <td>MT-TV</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000210082</td>\n",
       "      <td>MT-RNR2</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000209082</td>\n",
       "      <td>MT-TL1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284509</th>\n",
       "      <td>ENSG00000198216</td>\n",
       "      <td>CACNA1E</td>\n",
       "      <td>777</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284510</th>\n",
       "      <td>ENSG00000198216</td>\n",
       "      <td>CACNA1E</td>\n",
       "      <td>777</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284511</th>\n",
       "      <td>ENSG00000198216</td>\n",
       "      <td>CACNA1E</td>\n",
       "      <td>777</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284512</th>\n",
       "      <td>ENSG00000159388</td>\n",
       "      <td>BTG2</td>\n",
       "      <td>7832</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284513</th>\n",
       "      <td>ENSG00000159388</td>\n",
       "      <td>BTG2</td>\n",
       "      <td>7832</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>284514 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   ensg     symb  entr\n",
       "0       ENSG00000210049    MT-TF   NaN\n",
       "1       ENSG00000211459  MT-RNR1   NaN\n",
       "2       ENSG00000210077    MT-TV   NaN\n",
       "3       ENSG00000210082  MT-RNR2   NaN\n",
       "4       ENSG00000209082   MT-TL1   NaN\n",
       "...                 ...      ...   ...\n",
       "284509  ENSG00000198216  CACNA1E   777\n",
       "284510  ENSG00000198216  CACNA1E   777\n",
       "284511  ENSG00000198216  CACNA1E   777\n",
       "284512  ENSG00000159388     BTG2  7832\n",
       "284513  ENSG00000159388     BTG2  7832\n",
       "\n",
       "[284514 rows x 3 columns]"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "biomart"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "id": "f9e3086e",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:13:22.380609Z",
     "start_time": "2022-12-23T18:13:22.279991Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "209401"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "biomart.duplicated().sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "8400db46",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T18:12:02.051592Z",
     "start_time": "2022-12-23T18:12:02.009121Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "400960       296\n",
       "388815       258\n",
       "7917         231\n",
       "3805         192\n",
       "5602         192\n",
       "            ... \n",
       "101928288      1\n",
       "100287932      1\n",
       "100874035      1\n",
       "155038         1\n",
       "4535           1\n",
       "Name: entr, Length: 27206, dtype: int64"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "biomart.entr.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "6fc900b7",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T16:27:39.484387Z",
     "start_time": "2022-12-23T16:27:39.479340Z"
    }
   },
   "outputs": [],
   "source": [
    "import requests\n",
    "from tqdm import tqdm\n",
    "\n",
    "\n",
    "def download(url: str, fname: str):\n",
    "    resp = requests.get(url, stream=True)\n",
    "    total = int(resp.headers.get('content-length', 0))\n",
    "    # Can also replace 'file' with a io.BytesIO object\n",
    "    with open(fname, 'wb') as file, tqdm(\n",
    "        desc=fname,\n",
    "        total=total,\n",
    "        unit='iB',\n",
    "        unit_scale=True,\n",
    "        unit_divisor=1024,\n",
    "    ) as bar:\n",
    "        for data in resp.iter_content(chunk_size=1024):\n",
    "            size = file.write(data)\n",
    "            bar.update(size)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "6e209846",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-23T16:27:35.670156Z",
     "start_time": "2022-12-23T16:27:26.983898Z"
    }
   },
   "outputs": [
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[18], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mdownload\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mhttp://www.ensembl.org/biomart/martservice?query=<?xml version=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m1.0\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m encoding=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mUTF-8\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m?><!DOCTYPE Query><Query  virtualSchemaName = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdefault\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m formatter = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTSV\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m header = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m0\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m uniqueRows = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m0\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m count = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m datasetConfigVersion = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m0.6\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m ><Dataset name = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mhsapiens_gene_ensembl\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m interface = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdefault\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m ><Attribute name = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mensembl_gene_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m /><Attribute name = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mexternal_gene_name\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m /><Attribute name = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtranscript_is_canonical\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m /><Attribute name = \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mentrezgene_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m /></Dataset></Query>\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m/Users/reema/Postdoc/Temp/results.txt\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n",
      "Cell \u001b[0;32mIn[17], line 6\u001b[0m, in \u001b[0;36mdownload\u001b[0;34m(url, fname)\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdownload\u001b[39m(url: \u001b[38;5;28mstr\u001b[39m, fname: \u001b[38;5;28mstr\u001b[39m):\n\u001b[0;32m----> 6\u001b[0m     resp \u001b[38;5;241m=\u001b[39m \u001b[43mrequests\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m      7\u001b[0m     total \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mint\u001b[39m(resp\u001b[38;5;241m.\u001b[39mheaders\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcontent-length\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;241m0\u001b[39m))\n\u001b[1;32m      8\u001b[0m     \u001b[38;5;66;03m# Can also replace 'file' with a io.BytesIO object\u001b[39;00m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/requests/api.py:73\u001b[0m, in \u001b[0;36mget\u001b[0;34m(url, params, **kwargs)\u001b[0m\n\u001b[1;32m     62\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget\u001b[39m(url, params\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     63\u001b[0m     \u001b[38;5;124mr\u001b[39m\u001b[38;5;124;03m\"\"\"Sends a GET request.\u001b[39;00m\n\u001b[1;32m     64\u001b[0m \n\u001b[1;32m     65\u001b[0m \u001b[38;5;124;03m    :param url: URL for the new :class:`Request` object.\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     70\u001b[0m \u001b[38;5;124;03m    :rtype: requests.Response\u001b[39;00m\n\u001b[1;32m     71\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[0;32m---> 73\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mget\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparams\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/requests/api.py:59\u001b[0m, in \u001b[0;36mrequest\u001b[0;34m(method, url, **kwargs)\u001b[0m\n\u001b[1;32m     55\u001b[0m \u001b[38;5;66;03m# By using the 'with' statement we are sure the session is closed, thus we\u001b[39;00m\n\u001b[1;32m     56\u001b[0m \u001b[38;5;66;03m# avoid leaving sockets open which can trigger a ResourceWarning in some\u001b[39;00m\n\u001b[1;32m     57\u001b[0m \u001b[38;5;66;03m# cases, and look like a memory leak in others.\u001b[39;00m\n\u001b[1;32m     58\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m sessions\u001b[38;5;241m.\u001b[39mSession() \u001b[38;5;28;01mas\u001b[39;00m session:\n\u001b[0;32m---> 59\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msession\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmethod\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/requests/sessions.py:587\u001b[0m, in \u001b[0;36mSession.request\u001b[0;34m(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)\u001b[0m\n\u001b[1;32m    582\u001b[0m send_kwargs \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m    583\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtimeout\u001b[39m\u001b[38;5;124m\"\u001b[39m: timeout,\n\u001b[1;32m    584\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mallow_redirects\u001b[39m\u001b[38;5;124m\"\u001b[39m: allow_redirects,\n\u001b[1;32m    585\u001b[0m }\n\u001b[1;32m    586\u001b[0m send_kwargs\u001b[38;5;241m.\u001b[39mupdate(settings)\n\u001b[0;32m--> 587\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[43mprep\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43msend_kwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    589\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m resp\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/requests/sessions.py:745\u001b[0m, in \u001b[0;36mSession.send\u001b[0;34m(self, request, **kwargs)\u001b[0m\n\u001b[1;32m    742\u001b[0m         \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m    744\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m stream:\n\u001b[0;32m--> 745\u001b[0m     \u001b[43mr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcontent\u001b[49m\n\u001b[1;32m    747\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m r\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/requests/models.py:899\u001b[0m, in \u001b[0;36mResponse.content\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    897\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_content \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m    898\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 899\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_content \u001b[38;5;241m=\u001b[39m \u001b[38;5;124;43mb\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mjoin\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43miter_content\u001b[49m\u001b[43m(\u001b[49m\u001b[43mCONTENT_CHUNK_SIZE\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    901\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_content_consumed \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m    902\u001b[0m \u001b[38;5;66;03m# don't need to release the connection; that's been handled by urllib3\u001b[39;00m\n\u001b[1;32m    903\u001b[0m \u001b[38;5;66;03m# since we exhausted the data.\u001b[39;00m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/requests/models.py:816\u001b[0m, in \u001b[0;36mResponse.iter_content.<locals>.generate\u001b[0;34m()\u001b[0m\n\u001b[1;32m    814\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mraw, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstream\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m    815\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 816\u001b[0m         \u001b[38;5;28;01myield from\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mraw\u001b[38;5;241m.\u001b[39mstream(chunk_size, decode_content\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m    817\u001b[0m     \u001b[38;5;28;01mexcept\u001b[39;00m ProtocolError \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m    818\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m ChunkedEncodingError(e)\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/urllib3/response.py:624\u001b[0m, in \u001b[0;36mHTTPResponse.stream\u001b[0;34m(self, amt, decode_content)\u001b[0m\n\u001b[1;32m    608\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    609\u001b[0m \u001b[38;5;124;03mA generator wrapper for the read() method. A call will block until\u001b[39;00m\n\u001b[1;32m    610\u001b[0m \u001b[38;5;124;03m``amt`` bytes have been read from the connection or until the\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    621\u001b[0m \u001b[38;5;124;03m    'content-encoding' header.\u001b[39;00m\n\u001b[1;32m    622\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    623\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mchunked \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msupports_chunked_reads():\n\u001b[0;32m--> 624\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mread_chunked(amt, decode_content\u001b[38;5;241m=\u001b[39mdecode_content):\n\u001b[1;32m    625\u001b[0m         \u001b[38;5;28;01myield\u001b[39;00m line\n\u001b[1;32m    626\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/urllib3/response.py:828\u001b[0m, in \u001b[0;36mHTTPResponse.read_chunked\u001b[0;34m(self, amt, decode_content)\u001b[0m\n\u001b[1;32m    825\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[1;32m    827\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m--> 828\u001b[0m     \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_update_chunk_length\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    829\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mchunk_left \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m    830\u001b[0m         \u001b[38;5;28;01mbreak\u001b[39;00m\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/site-packages/urllib3/response.py:758\u001b[0m, in \u001b[0;36mHTTPResponse._update_chunk_length\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    756\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mchunk_left \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m    757\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[0;32m--> 758\u001b[0m line \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mreadline\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    759\u001b[0m line \u001b[38;5;241m=\u001b[39m line\u001b[38;5;241m.\u001b[39msplit(\u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m;\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;241m1\u001b[39m)[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m    760\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n",
      "File \u001b[0;32m~/anaconda2/envs/biorosetta/lib/python3.10/socket.py:705\u001b[0m, in \u001b[0;36mSocketIO.readinto\u001b[0;34m(self, b)\u001b[0m\n\u001b[1;32m    703\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[1;32m    704\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 705\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sock\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrecv_into\u001b[49m\u001b[43m(\u001b[49m\u001b[43mb\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    706\u001b[0m     \u001b[38;5;28;01mexcept\u001b[39;00m timeout:\n\u001b[1;32m    707\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_timeout_occurred \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "download('http://www.ensembl.org/biomart/martservice?query=<?xml version=\"1.0\" encoding=\"UTF-8\"?><!DOCTYPE Query><Query  virtualSchemaName = \"default\" formatter = \"TSV\" header = \"0\" uniqueRows = \"0\" count = \"\" datasetConfigVersion = \"0.6\" ><Dataset name = \"hsapiens_gene_ensembl\" interface = \"default\" ><Attribute name = \"ensembl_gene_id\" /><Attribute name = \"external_gene_name\" /><Attribute name = \"transcript_is_canonical\" /><Attribute name = \"entrezgene_id\" /></Dataset></Query>','/Users/reema/Postdoc/Temp/results.txt')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "id": "92fe69ca",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T20:57:52.155385Z",
     "start_time": "2022-12-28T20:57:52.150209Z"
    }
   },
   "outputs": [],
   "source": [
    "lookup = pd.DataFrame([['ciao','Zio'],['pippo','Pluto'],['tizio','caio']],columns=['id1','id3']).set_index('id1').squeeze()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "id": "104449c3",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T20:57:52.721121Z",
     "start_time": "2022-12-28T20:57:52.702386Z"
    }
   },
   "outputs": [],
   "source": [
    "add = pd.DataFrame([['ciao','zio'],\n",
    "                    ['ciao','zio'],\n",
    "                    ['prova','sbagliata'],\n",
    "                    ['prova2','sbagliata'],\n",
    "                    ['prova','sbagliata'],\n",
    "                      ['ciao','zio2'],\n",
    "                      ['ciao','zio3'],\n",
    "                      ['pippo','pluto'],\n",
    "                      ['pippo','pluto2']]\n",
    "                     ,columns=['id1','id2'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "id": "680c9338",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T20:57:53.119025Z",
     "start_time": "2022-12-28T20:57:53.085505Z"
    }
   },
   "outputs": [],
   "source": [
    "data = add\n",
    "id_orig = 'id1'\n",
    "id_synonym = 'id2'\n",
    "id_out = 'id3'\n",
    "pruned = data[data[id_orig].notna() & data[id_synonym].notna()]\n",
    "pruned = pruned[~pruned.duplicated(subset=[id_orig, id_synonym])]\n",
    "pruned = pruned[~pruned.duplicated(subset=[id_synonym], keep=False)] # we just remove inconsistent synonyms\n",
    "pruned_curr = pruned.loc[~pruned[id_synonym].isin(lookup.index)].copy()\n",
    "pruned_curr[id_out] = lookup.loc[pruned[id_orig].values].values\n",
    "pruned_curr = pruned_curr.set_index(id_synonym)[id_out].squeeze()\n",
    "new_lookup = pd.concat([lookup,pruned_curr])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "id": "52a0266e",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T20:57:53.857142Z",
     "start_time": "2022-12-28T20:57:53.847495Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "id2\n",
      "zio         Zio\n",
      "zio2        Zio\n",
      "zio3        Zio\n",
      "pluto     Pluto\n",
      "pluto2    Pluto\n",
      "Name: id3, dtype: object\n",
      "\n",
      "id1\n",
      "ciao       Zio\n",
      "pippo    Pluto\n",
      "tizio     caio\n",
      "Name: id3, dtype: object\n"
     ]
    }
   ],
   "source": [
    "print(pruned_curr)\n",
    "print()\n",
    "print(lookup)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "id": "e20b8c2f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2022-12-28T20:57:56.628878Z",
     "start_time": "2022-12-28T20:57:56.620729Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ciao        Zio\n",
       "pippo     Pluto\n",
       "tizio      caio\n",
       "zio         Zio\n",
       "zio2        Zio\n",
       "zio3        Zio\n",
       "pluto     Pluto\n",
       "pluto2    Pluto\n",
       "Name: id3, dtype: object"
      ]
     },
     "execution_count": 71,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_lookup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4c3ff16c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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   "title_cell": "Table of Contents",
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