merge_integration_results.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This script process DNA and RNA  integration results and merge them together side by side. It is written for Cervical project."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 369,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import matplotlib\n",
    "import seaborn\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from scipy.stats import ttest_ind\n",
    "import scipy.stats as ss\n",
    "from matplotlib import style\n",
    "matplotlib.style.use('ggplot')\n",
    "%matplotlib inline\n",
    "matplotlib.rcParams['figure.figsize'] = (15, 9)\n",
    "import pandas as pd\n",
    "# figure out number of indels"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This function process group by object, combine all rows with the same index into one row"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 422,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "def process_grp_bk(grp):\n",
    "    _df_or_sr = grp.apply(lambda col: ';'.join(col.unique().tolist()))\n",
    "#     _df_or_sr = grp.apply(combine_rows)\n",
    "    _df = _df_or_sr.to_frame().T\n",
    "#     _df_or_sr = grp.apply(lambda col: tuple(col.unique().tolist()))\n",
    "#     _df_or_sr = grp.apply(lambda col: set(col.values.tolist()))\n",
    "#     if grp.shape[0] == 1:\n",
    "#         _df = _df_or_sr.to_frame().T\n",
    "#     else: # grp.shape[0] > 1 \n",
    "#         _df = _df_or_sr.to_frame().T\n",
    "#     print(_df.shape)    \n",
    "    assert _df.shape[0] == 1\n",
    "#     if _df.shape[0] > 1:\n",
    "#         print(_df)\n",
    "    return _df\n",
    "\n",
    "def process_grp(grp):\n",
    "    _df_or_sr = grp.apply(lambda col: ';'.join(col.unique().tolist()))\n",
    "    _df = _df_or_sr.to_frame().T\n",
    "    assert _df.shape[0] == 1\n",
    "    return _df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 424,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(271, 7)\n",
      "(226, 7)\n"
     ]
    }
   ],
   "source": [
    "RNA_integration = pd.read_csv('/projects/trans_scratch/validations/workspace/szong/Cervical/integration/82_patients/genome/genome_integration_summary.csv.added', sep='\\t')\n",
    "print(RNA_integration.shape)\n",
    "RNA_integration = RNA_integration[RNA_integration['virus'] != 'No-Hits']\n",
    "print(RNA_integration.shape)\n",
    "# RNA_integration\n",
    "\n",
    "RNA_GRP = RNA_integration.groupby(['patient', 'virus']).apply(process_grp).reset_index(level=2, drop=True)\n",
    "del RNA_GRP['patient']\n",
    "del RNA_GRP['virus']\n",
    "# RNA_GRP\n",
    "RNA_GRP.reset_index(inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 425,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(520, 6)\n",
      "(513, 6)\n"
     ]
    }
   ],
   "source": [
    "DNA_integration = pd.read_csv('/projects/trans_scratch/validations/workspace/szong/Cervical/integration/82_patients/transcriptome/transcriptome_integration_summary.csv.added', sep='\\t')\n",
    "print(DNA_integration.shape)\n",
    "DNA_integration = DNA_integration[DNA_integration['virus'] != 'No-Hits']\n",
    "print(DNA_integration.shape)\n",
    "\n",
    "# DNA_integration.groupby(['patient', 'virus']).apply(process_grp).head().reset_index(level=2, drop=True)\n",
    "DNA_GRP = DNA_integration.groupby(['patient', 'virus']).apply(process_grp).reset_index(level=2, drop=True)\n",
    "del DNA_GRP['patient']\n",
    "del DNA_GRP['virus']\n",
    "# DNA_GRP\n",
    "DNA_GRP.reset_index(inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 426,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>patient</th>\n",
       "      <th>virus</th>\n",
       "      <th>library</th>\n",
       "      <th>Integration</th>\n",
       "      <th>human-breakpoint</th>\n",
       "      <th>gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HTMCP-03-06-02001</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37700</td>\n",
       "      <td>YES</td>\n",
       "      <td>3_189526056;3_189526059;3_189526315;3_18952631...</td>\n",
       "      <td>TP63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HTMCP-03-06-02002</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>A37701</td>\n",
       "      <td>YES</td>\n",
       "      <td>22_43161525;22_43161526;22_43163674;22_4316513...</td>\n",
       "      <td>intergenic</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HTMCP-03-06-02003</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37702</td>\n",
       "      <td>YES</td>\n",
       "      <td>11_60882522;11_60935033</td>\n",
       "      <td>CD5;intergenic</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HTMCP-03-06-02006</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37704</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HTMCP-03-06-02006</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A37704</td>\n",
       "      <td>YES</td>\n",
       "      <td>12_46287201;12_46328672;12_46329948;12_4633703...</td>\n",
       "      <td>ARID2;SCAF11</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             patient                         virus library Integration  \\\n",
       "0  HTMCP-03-06-02001  Human papillomavirus type 16  A37700         YES   \n",
       "1  HTMCP-03-06-02002  Human papillomavirus type 52  A37701         YES   \n",
       "2  HTMCP-03-06-02003  Human papillomavirus type 16  A37702         YES   \n",
       "3  HTMCP-03-06-02006  Human papillomavirus type 18  A37704          NO   \n",
       "4  HTMCP-03-06-02006  Human papillomavirus type 45  A37704         YES   \n",
       "\n",
       "                                    human-breakpoint            gene  \n",
       "0  3_189526056;3_189526059;3_189526315;3_18952631...            TP63  \n",
       "1  22_43161525;22_43161526;22_43163674;22_4316513...      intergenic  \n",
       "2                            11_60882522;11_60935033  CD5;intergenic  \n",
       "3                                                  -               -  \n",
       "4  12_46287201;12_46328672;12_46329948;12_4633703...    ARID2;SCAF11  "
      ]
     },
     "execution_count": 426,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DNA_GRP.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 427,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>patient</th>\n",
       "      <th>virus</th>\n",
       "      <th>external</th>\n",
       "      <th>Integration</th>\n",
       "      <th>human-breakpoint</th>\n",
       "      <th>gene</th>\n",
       "      <th>library</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HTMCP-03-06-02003</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>HTMCP_126</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37236</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 34</td>\n",
       "      <td>HTMCP_133</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 73</td>\n",
       "      <td>HTMCP_133</td>\n",
       "      <td>YES</td>\n",
       "      <td>17_36310359</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>A37243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HTMCP-03-06-02036</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>HTMCP_142</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37252</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HTMCP-03-06-02037</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>HTMCP_143</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37253</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             patient                         virus   external Integration  \\\n",
       "0  HTMCP-03-06-02003  Human papillomavirus type 16  HTMCP_126          NO   \n",
       "1  HTMCP-03-06-02012  Human papillomavirus type 34  HTMCP_133          NO   \n",
       "2  HTMCP-03-06-02012  Human papillomavirus type 73  HTMCP_133         YES   \n",
       "3  HTMCP-03-06-02036  Human papillomavirus type 16  HTMCP_142          NO   \n",
       "4  HTMCP-03-06-02037  Human papillomavirus type 52  HTMCP_143          NO   \n",
       "\n",
       "  human-breakpoint        gene library  \n",
       "0                -           -  A37236  \n",
       "1                -           -  A37243  \n",
       "2      17_36310359  intergenic  A37243  \n",
       "3                -           -  A37252  \n",
       "4                -           -  A37253  "
      ]
     },
     "execution_count": 427,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "RNA_GRP.head()\n",
    "# ?pd.merge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 428,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>patient</th>\n",
       "      <th>virus</th>\n",
       "      <th>library_RNA</th>\n",
       "      <th>Integration_RNA</th>\n",
       "      <th>human-breakpoint_RNA</th>\n",
       "      <th>gene_RNA</th>\n",
       "      <th>external</th>\n",
       "      <th>Integration_DNA</th>\n",
       "      <th>human-breakpoint_DNA</th>\n",
       "      <th>gene_DNA</th>\n",
       "      <th>library_DNA</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HTMCP-03-06-02001</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37700</td>\n",
       "      <td>YES</td>\n",
       "      <td>3_189526056;3_189526059;3_189526315;3_18952631...</td>\n",
       "      <td>TP63</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HTMCP-03-06-02002</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>A37701</td>\n",
       "      <td>YES</td>\n",
       "      <td>22_43161525;22_43161526;22_43163674;22_4316513...</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HTMCP-03-06-02003</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37702</td>\n",
       "      <td>YES</td>\n",
       "      <td>11_60882522;11_60935033</td>\n",
       "      <td>CD5;intergenic</td>\n",
       "      <td>HTMCP_126</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37236</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HTMCP-03-06-02006</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37704</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HTMCP-03-06-02006</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A37704</td>\n",
       "      <td>YES</td>\n",
       "      <td>12_46287201;12_46328672;12_46329948;12_4633703...</td>\n",
       "      <td>ARID2;SCAF11</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>HTMCP-03-06-02008</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37706</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>HTMCP-03-06-02008</td>\n",
       "      <td>Human papillomavirus type 9</td>\n",
       "      <td>A37706</td>\n",
       "      <td>YES</td>\n",
       "      <td>9_115288280</td>\n",
       "      <td>KIAA1958</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37707</td>\n",
       "      <td>YES</td>\n",
       "      <td>14_38057528;14_38057621</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37707</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 34</td>\n",
       "      <td>A37707</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>HTMCP_133</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 58</td>\n",
       "      <td>A37707</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>HTMCP-03-06-02012</td>\n",
       "      <td>Human papillomavirus type 73</td>\n",
       "      <td>A37707</td>\n",
       "      <td>YES</td>\n",
       "      <td>17_36285541;17_36347084;17_36401125;6_92985326</td>\n",
       "      <td>TBC1D3;TBC1D3,LOC440434;LOC440434;intergenic</td>\n",
       "      <td>HTMCP_133</td>\n",
       "      <td>YES</td>\n",
       "      <td>17_36310359</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>A37243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>HTMCP-03-06-02013</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37708</td>\n",
       "      <td>YES</td>\n",
       "      <td>3_59738049;3_59908142;3_59908143;3_59999804;3_...</td>\n",
       "      <td>FHIT</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>HTMCP-03-06-02020</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37710</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>HTMCP-03-06-02020</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A37710</td>\n",
       "      <td>YES</td>\n",
       "      <td>13_73972085;13_73973165;2_62646172;4_103340147...</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>HTMCP-03-06-02036</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37714</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>HTMCP_142</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37252</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>HTMCP-03-06-02037</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>A37715</td>\n",
       "      <td>YES</td>\n",
       "      <td>6_157714033;6_157731388;6_157731411;6_15773531...</td>\n",
       "      <td>TMEM242</td>\n",
       "      <td>HTMCP_143</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>HTMCP-03-06-02040</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>A37716</td>\n",
       "      <td>YES</td>\n",
       "      <td>13_75085093;13_75085094;13_75085544</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>HTMCP-03-06-02042</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37717</td>\n",
       "      <td>YES</td>\n",
       "      <td>1_150997084;1_150997085;1_150997988;1_15099970...</td>\n",
       "      <td>PRUNE;CDC42SE1;MLLT11</td>\n",
       "      <td>HTMCP_145</td>\n",
       "      <td>YES</td>\n",
       "      <td>1_151029494;1_151029496</td>\n",
       "      <td>CDC42SE1</td>\n",
       "      <td>A37255</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>HTMCP-03-06-02046</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37718</td>\n",
       "      <td>YES</td>\n",
       "      <td>19_1181971;19_1182527;19_1183716;19_1184195;19...</td>\n",
       "      <td>intergenic;STK11</td>\n",
       "      <td>HTMCP_147</td>\n",
       "      <td>YES</td>\n",
       "      <td>19_1181971;19_1183502;19_1192727</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>A37257</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>HTMCP-03-06-02046</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A37718</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>HTMCP-03-06-02047</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37719</td>\n",
       "      <td>YES</td>\n",
       "      <td>13_74263236;13_74269594;13_74269810;13_7428966...</td>\n",
       "      <td>KLF12;BC037497</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>HTMCP-03-06-02054</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>A37720</td>\n",
       "      <td>YES</td>\n",
       "      <td>14_87398614;1_93913863;1_93926370;8_42394076;8...</td>\n",
       "      <td>intergenic;FNBP1L;SLC20A2;SMIM19</td>\n",
       "      <td>HTMCP_149</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A37259</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>HTMCP-03-06-02057</td>\n",
       "      <td>Human papillomavirus type 58</td>\n",
       "      <td>A37721</td>\n",
       "      <td>YES</td>\n",
       "      <td>17_39605438;17_39616493;17_39616494;17_39618596</td>\n",
       "      <td>intergenic;KRT32</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>HTMCP-03-06-02058</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37722</td>\n",
       "      <td>YES</td>\n",
       "      <td>8_128289076;8_128302305;8_128302307;8_12830230...</td>\n",
       "      <td>intergenic;DQ515899,DQ515898,LOC727677</td>\n",
       "      <td>HTMCP_151</td>\n",
       "      <td>YES</td>\n",
       "      <td>18_37408866;8_128319365;8_128323246</td>\n",
       "      <td>intergenic;DQ515899,DQ515898,LOC727677</td>\n",
       "      <td>A37261</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>HTMCP-03-06-02061</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37724</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>HTMCP-03-06-02063</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A37725</td>\n",
       "      <td>YES</td>\n",
       "      <td>2_142008770;2_142008771;2_142009078;2_14201026...</td>\n",
       "      <td>LRP1B;SERHL2</td>\n",
       "      <td>HTMCP_156</td>\n",
       "      <td>YES</td>\n",
       "      <td>2_141933994;2_142008771;22_42896541</td>\n",
       "      <td>LRP1B;intergenic</td>\n",
       "      <td>A37266</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>HTMCP-03-06-02068</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A37726</td>\n",
       "      <td>YES</td>\n",
       "      <td>1_209555780;1_209557136;1_209557664;1_20955804...</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>HTMCP-03-06-02068</td>\n",
       "      <td>Human papillomavirus type 59</td>\n",
       "      <td>A37726</td>\n",
       "      <td>YES</td>\n",
       "      <td>1_209560518</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>HTMCP-03-06-02070</td>\n",
       "      <td>Human papillomavirus type 31</td>\n",
       "      <td>A37727</td>\n",
       "      <td>YES</td>\n",
       "      <td>4_74572294;4_74572295;4_74581281;4_74581283;4_...</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>91</th>\n",
       "      <td>HTMCP-03-06-02209</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A52364</td>\n",
       "      <td>YES</td>\n",
       "      <td>10_114084136;10_114172408;10_114178613;10_1141...</td>\n",
       "      <td>GUCY2GP;ACSL5</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>92</th>\n",
       "      <td>HTMCP-03-06-02210</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A52365</td>\n",
       "      <td>YES</td>\n",
       "      <td>10_99063964;10_99067275;10_99071147;10_9907115...</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>HTMCP_307</td>\n",
       "      <td>YES</td>\n",
       "      <td>10_99063964</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>A52339</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93</th>\n",
       "      <td>HTMCP-03-06-02213</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A54479</td>\n",
       "      <td>YES</td>\n",
       "      <td>11_30439182;17_54317289;3_191861919;3_19217786...</td>\n",
       "      <td>MPPED2;ANKFN1;FGF12</td>\n",
       "      <td>HTMCP_309</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A54387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>94</th>\n",
       "      <td>HTMCP-03-06-02214</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A52366</td>\n",
       "      <td>YES</td>\n",
       "      <td>4_87540666</td>\n",
       "      <td>PTPN13</td>\n",
       "      <td>HTMCP_310</td>\n",
       "      <td>YES</td>\n",
       "      <td>4_87540666;4_87644435</td>\n",
       "      <td>PTPN13</td>\n",
       "      <td>A52340</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>HTMCP-03-06-02215</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A52367</td>\n",
       "      <td>YES</td>\n",
       "      <td>9_85677563;9_85682815;9_85682834;9_85682978;9_...</td>\n",
       "      <td>RASEF;intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>HTMCP-03-06-02216</td>\n",
       "      <td>Human papillomavirus type 59</td>\n",
       "      <td>A54480</td>\n",
       "      <td>YES</td>\n",
       "      <td>18_61173195;18_61173674;18_61173676</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>HTMCP-03-06-02217</td>\n",
       "      <td>Alphapapillomavirus 9</td>\n",
       "      <td>A57115</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>HTMCP-03-06-02217</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A57115</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99</th>\n",
       "      <td>HTMCP-03-06-02219</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A57116</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>100</th>\n",
       "      <td>HTMCP-03-06-02219</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A57116</td>\n",
       "      <td>YES</td>\n",
       "      <td>1_209616413;1_209636146</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101</th>\n",
       "      <td>HTMCP-03-06-02219</td>\n",
       "      <td>Human papillomavirus type 97</td>\n",
       "      <td>A57116</td>\n",
       "      <td>YES</td>\n",
       "      <td>1_209616413</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102</th>\n",
       "      <td>HTMCP-03-06-02225</td>\n",
       "      <td>Human papillomavirus type 51</td>\n",
       "      <td>A57118</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103</th>\n",
       "      <td>HTMCP-03-06-02225</td>\n",
       "      <td>Human papillomavirus type 69</td>\n",
       "      <td>A57118</td>\n",
       "      <td>YES</td>\n",
       "      <td>6_127149181;6_127149190;6_127150024;6_12715539...</td>\n",
       "      <td>AK127472;intergenic</td>\n",
       "      <td>HTMCP_406</td>\n",
       "      <td>YES</td>\n",
       "      <td>6_127148053</td>\n",
       "      <td>AK127472</td>\n",
       "      <td>A57091</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104</th>\n",
       "      <td>HTMCP-03-06-02225</td>\n",
       "      <td>Human papillomavirus type 82</td>\n",
       "      <td>A57118</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105</th>\n",
       "      <td>HTMCP-03-06-02230</td>\n",
       "      <td>Human papillomavirus type 51</td>\n",
       "      <td>A57119</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106</th>\n",
       "      <td>HTMCP-03-06-02230</td>\n",
       "      <td>Human papillomavirus type 82</td>\n",
       "      <td>A57119</td>\n",
       "      <td>YES</td>\n",
       "      <td>2_227659704</td>\n",
       "      <td>IRS1</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>107</th>\n",
       "      <td>HTMCP-03-06-02235</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A57120</td>\n",
       "      <td>YES</td>\n",
       "      <td>X_107745851;X_107745853;X_107777748;X_10777777...</td>\n",
       "      <td>COL4A5;intergenic;IRS4</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108</th>\n",
       "      <td>HTMCP-03-06-02238</td>\n",
       "      <td>Human papillomavirus type 18</td>\n",
       "      <td>A57121</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>HTMCP_409</td>\n",
       "      <td>YES</td>\n",
       "      <td>15_72233495;15_72236104;16_79363861;16_7942275...</td>\n",
       "      <td>MYO9A;intergenic;COL6A3;LRRFIP1</td>\n",
       "      <td>A57094</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109</th>\n",
       "      <td>HTMCP-03-06-02239</td>\n",
       "      <td>Alphapapillomavirus 9</td>\n",
       "      <td>A57122</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110</th>\n",
       "      <td>HTMCP-03-06-02239</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A57122</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>111</th>\n",
       "      <td>HTMCP-03-06-02240</td>\n",
       "      <td>Alphapapillomavirus 9</td>\n",
       "      <td>A57123</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>112</th>\n",
       "      <td>HTMCP-03-06-02240</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>A57123</td>\n",
       "      <td>YES</td>\n",
       "      <td>5_1339122;5_1341678;5_1341685;5_1341686;5_1341...</td>\n",
       "      <td>CLPTM1L;intergenic</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113</th>\n",
       "      <td>HTMCP-03-06-02242</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>A57124</td>\n",
       "      <td>YES</td>\n",
       "      <td>17_57926025;17_57926026;17_57926029;17_5792614...</td>\n",
       "      <td>intergenic;TUBD1</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114</th>\n",
       "      <td>HTMCP-03-06-02098</td>\n",
       "      <td>Human papillomavirus type 9</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_174</td>\n",
       "      <td>YES</td>\n",
       "      <td>2_137648071</td>\n",
       "      <td>THSD7B</td>\n",
       "      <td>A37284</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115</th>\n",
       "      <td>HTMCP-03-06-02103</td>\n",
       "      <td>Human papillomavirus type 53</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_230</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A38427</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>HTMCP-03-06-02110</td>\n",
       "      <td>Human papillomavirus type 45</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_235</td>\n",
       "      <td>YES</td>\n",
       "      <td>8_128302005</td>\n",
       "      <td>DQ515899,DQ515898,LOC727677</td>\n",
       "      <td>A38432</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117</th>\n",
       "      <td>HTMCP-03-06-02145</td>\n",
       "      <td>Human papillomavirus type 9</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_249</td>\n",
       "      <td>YES</td>\n",
       "      <td>18_28136581</td>\n",
       "      <td>intergenic</td>\n",
       "      <td>A38446</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>118</th>\n",
       "      <td>HTMCP-03-06-02156</td>\n",
       "      <td>Human papillomavirus type 16</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_281</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A52320</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>119</th>\n",
       "      <td>HTMCP-03-06-02156</td>\n",
       "      <td>Human papillomavirus type 52</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_281</td>\n",
       "      <td>NO</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>A52320</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120</th>\n",
       "      <td>HTMCP-03-06-02179</td>\n",
       "      <td>Human papillomavirus type 97</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>na</td>\n",
       "      <td>HTMCP_290</td>\n",
       "      <td>YES</td>\n",
       "      <td>6_3289268</td>\n",
       "      <td>SLC22A23,CFB,TNXB,C4B_2,C2,HSPA1L</td>\n",
       "      <td>A54381</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>121 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               patient                         virus library_RNA  \\\n",
       "0    HTMCP-03-06-02001  Human papillomavirus type 16      A37700   \n",
       "1    HTMCP-03-06-02002  Human papillomavirus type 52      A37701   \n",
       "2    HTMCP-03-06-02003  Human papillomavirus type 16      A37702   \n",
       "3    HTMCP-03-06-02006  Human papillomavirus type 18      A37704   \n",
       "4    HTMCP-03-06-02006  Human papillomavirus type 45      A37704   \n",
       "5    HTMCP-03-06-02008  Human papillomavirus type 16      A37706   \n",
       "6    HTMCP-03-06-02008   Human papillomavirus type 9      A37706   \n",
       "7    HTMCP-03-06-02012  Human papillomavirus type 16      A37707   \n",
       "8    HTMCP-03-06-02012  Human papillomavirus type 18      A37707   \n",
       "9    HTMCP-03-06-02012  Human papillomavirus type 34      A37707   \n",
       "10   HTMCP-03-06-02012  Human papillomavirus type 58      A37707   \n",
       "11   HTMCP-03-06-02012  Human papillomavirus type 73      A37707   \n",
       "12   HTMCP-03-06-02013  Human papillomavirus type 16      A37708   \n",
       "13   HTMCP-03-06-02020  Human papillomavirus type 18      A37710   \n",
       "14   HTMCP-03-06-02020  Human papillomavirus type 45      A37710   \n",
       "15   HTMCP-03-06-02036  Human papillomavirus type 16      A37714   \n",
       "16   HTMCP-03-06-02037  Human papillomavirus type 52      A37715   \n",
       "17   HTMCP-03-06-02040  Human papillomavirus type 52      A37716   \n",
       "18   HTMCP-03-06-02042  Human papillomavirus type 16      A37717   \n",
       "19   HTMCP-03-06-02046  Human papillomavirus type 16      A37718   \n",
       "20   HTMCP-03-06-02046  Human papillomavirus type 45      A37718   \n",
       "21   HTMCP-03-06-02047  Human papillomavirus type 18      A37719   \n",
       "22   HTMCP-03-06-02054  Human papillomavirus type 52      A37720   \n",
       "23   HTMCP-03-06-02057  Human papillomavirus type 58      A37721   \n",
       "24   HTMCP-03-06-02058  Human papillomavirus type 18      A37722   \n",
       "25   HTMCP-03-06-02061  Human papillomavirus type 16      A37724   \n",
       "26   HTMCP-03-06-02063  Human papillomavirus type 16      A37725   \n",
       "27   HTMCP-03-06-02068  Human papillomavirus type 18      A37726   \n",
       "28   HTMCP-03-06-02068  Human papillomavirus type 59      A37726   \n",
       "29   HTMCP-03-06-02070  Human papillomavirus type 31      A37727   \n",
       "..                 ...                           ...         ...   \n",
       "91   HTMCP-03-06-02209  Human papillomavirus type 16      A52364   \n",
       "92   HTMCP-03-06-02210  Human papillomavirus type 16      A52365   \n",
       "93   HTMCP-03-06-02213  Human papillomavirus type 16      A54479   \n",
       "94   HTMCP-03-06-02214  Human papillomavirus type 16      A52366   \n",
       "95   HTMCP-03-06-02215  Human papillomavirus type 16      A52367   \n",
       "96   HTMCP-03-06-02216  Human papillomavirus type 59      A54480   \n",
       "97   HTMCP-03-06-02217         Alphapapillomavirus 9      A57115   \n",
       "98   HTMCP-03-06-02217  Human papillomavirus type 16      A57115   \n",
       "99   HTMCP-03-06-02219  Human papillomavirus type 18      A57116   \n",
       "100  HTMCP-03-06-02219  Human papillomavirus type 45      A57116   \n",
       "101  HTMCP-03-06-02219  Human papillomavirus type 97      A57116   \n",
       "102  HTMCP-03-06-02225  Human papillomavirus type 51      A57118   \n",
       "103  HTMCP-03-06-02225  Human papillomavirus type 69      A57118   \n",
       "104  HTMCP-03-06-02225  Human papillomavirus type 82      A57118   \n",
       "105  HTMCP-03-06-02230  Human papillomavirus type 51      A57119   \n",
       "106  HTMCP-03-06-02230  Human papillomavirus type 82      A57119   \n",
       "107  HTMCP-03-06-02235  Human papillomavirus type 45      A57120   \n",
       "108  HTMCP-03-06-02238  Human papillomavirus type 18      A57121   \n",
       "109  HTMCP-03-06-02239         Alphapapillomavirus 9      A57122   \n",
       "110  HTMCP-03-06-02239  Human papillomavirus type 16      A57122   \n",
       "111  HTMCP-03-06-02240         Alphapapillomavirus 9      A57123   \n",
       "112  HTMCP-03-06-02240  Human papillomavirus type 16      A57123   \n",
       "113  HTMCP-03-06-02242  Human papillomavirus type 45      A57124   \n",
       "114  HTMCP-03-06-02098   Human papillomavirus type 9          na   \n",
       "115  HTMCP-03-06-02103  Human papillomavirus type 53          na   \n",
       "116  HTMCP-03-06-02110  Human papillomavirus type 45          na   \n",
       "117  HTMCP-03-06-02145   Human papillomavirus type 9          na   \n",
       "118  HTMCP-03-06-02156  Human papillomavirus type 16          na   \n",
       "119  HTMCP-03-06-02156  Human papillomavirus type 52          na   \n",
       "120  HTMCP-03-06-02179  Human papillomavirus type 97          na   \n",
       "\n",
       "    Integration_RNA                               human-breakpoint_RNA  \\\n",
       "0               YES  3_189526056;3_189526059;3_189526315;3_18952631...   \n",
       "1               YES  22_43161525;22_43161526;22_43163674;22_4316513...   \n",
       "2               YES                            11_60882522;11_60935033   \n",
       "3                NO                                                  -   \n",
       "4               YES  12_46287201;12_46328672;12_46329948;12_4633703...   \n",
       "5                NO                                                  -   \n",
       "6               YES                                        9_115288280   \n",
       "7               YES                            14_38057528;14_38057621   \n",
       "8                NO                                                  -   \n",
       "9                NO                                                  -   \n",
       "10               NO                                                  -   \n",
       "11              YES     17_36285541;17_36347084;17_36401125;6_92985326   \n",
       "12              YES  3_59738049;3_59908142;3_59908143;3_59999804;3_...   \n",
       "13               NO                                                  -   \n",
       "14              YES  13_73972085;13_73973165;2_62646172;4_103340147...   \n",
       "15               NO                                                  -   \n",
       "16              YES  6_157714033;6_157731388;6_157731411;6_15773531...   \n",
       "17              YES                13_75085093;13_75085094;13_75085544   \n",
       "18              YES  1_150997084;1_150997085;1_150997988;1_15099970...   \n",
       "19              YES  19_1181971;19_1182527;19_1183716;19_1184195;19...   \n",
       "20               NO                                                  -   \n",
       "21              YES  13_74263236;13_74269594;13_74269810;13_7428966...   \n",
       "22              YES  14_87398614;1_93913863;1_93926370;8_42394076;8...   \n",
       "23              YES    17_39605438;17_39616493;17_39616494;17_39618596   \n",
       "24              YES  8_128289076;8_128302305;8_128302307;8_12830230...   \n",
       "25               NO                                                  -   \n",
       "26              YES  2_142008770;2_142008771;2_142009078;2_14201026...   \n",
       "27              YES  1_209555780;1_209557136;1_209557664;1_20955804...   \n",
       "28              YES                                        1_209560518   \n",
       "29              YES  4_74572294;4_74572295;4_74581281;4_74581283;4_...   \n",
       "..              ...                                                ...   \n",
       "91              YES  10_114084136;10_114172408;10_114178613;10_1141...   \n",
       "92              YES  10_99063964;10_99067275;10_99071147;10_9907115...   \n",
       "93              YES  11_30439182;17_54317289;3_191861919;3_19217786...   \n",
       "94              YES                                         4_87540666   \n",
       "95              YES  9_85677563;9_85682815;9_85682834;9_85682978;9_...   \n",
       "96              YES                18_61173195;18_61173674;18_61173676   \n",
       "97               NO                                                  -   \n",
       "98               NO                                                  -   \n",
       "99               NO                                                  -   \n",
       "100             YES                            1_209616413;1_209636146   \n",
       "101             YES                                        1_209616413   \n",
       "102              NO                                                  -   \n",
       "103             YES  6_127149181;6_127149190;6_127150024;6_12715539...   \n",
       "104              NO                                                  -   \n",
       "105              NO                                                  -   \n",
       "106             YES                                        2_227659704   \n",
       "107             YES  X_107745851;X_107745853;X_107777748;X_10777777...   \n",
       "108              NO                                                  -   \n",
       "109              NO                                                  -   \n",
       "110              NO                                                  -   \n",
       "111              NO                                                  -   \n",
       "112             YES  5_1339122;5_1341678;5_1341685;5_1341686;5_1341...   \n",
       "113             YES  17_57926025;17_57926026;17_57926029;17_5792614...   \n",
       "114              na                                                 na   \n",
       "115              na                                                 na   \n",
       "116              na                                                 na   \n",
       "117              na                                                 na   \n",
       "118              na                                                 na   \n",
       "119              na                                                 na   \n",
       "120              na                                                 na   \n",
       "\n",
       "                                         gene_RNA   external Integration_DNA  \\\n",
       "0                                            TP63         na              na   \n",
       "1                                      intergenic         na              na   \n",
       "2                                  CD5;intergenic  HTMCP_126              NO   \n",
       "3                                               -         na              na   \n",
       "4                                    ARID2;SCAF11         na              na   \n",
       "5                                               -         na              na   \n",
       "6                                        KIAA1958         na              na   \n",
       "7                                      intergenic         na              na   \n",
       "8                                               -         na              na   \n",
       "9                                               -  HTMCP_133              NO   \n",
       "10                                              -         na              na   \n",
       "11   TBC1D3;TBC1D3,LOC440434;LOC440434;intergenic  HTMCP_133             YES   \n",
       "12                                           FHIT         na              na   \n",
       "13                                              -         na              na   \n",
       "14                                     intergenic         na              na   \n",
       "15                                              -  HTMCP_142              NO   \n",
       "16                                        TMEM242  HTMCP_143              NO   \n",
       "17                                     intergenic         na              na   \n",
       "18                          PRUNE;CDC42SE1;MLLT11  HTMCP_145             YES   \n",
       "19                               intergenic;STK11  HTMCP_147             YES   \n",
       "20                                              -         na              na   \n",
       "21                                 KLF12;BC037497         na              na   \n",
       "22               intergenic;FNBP1L;SLC20A2;SMIM19  HTMCP_149              NO   \n",
       "23                               intergenic;KRT32         na              na   \n",
       "24         intergenic;DQ515899,DQ515898,LOC727677  HTMCP_151             YES   \n",
       "25                                              -         na              na   \n",
       "26                                   LRP1B;SERHL2  HTMCP_156             YES   \n",
       "27                                     intergenic         na              na   \n",
       "28                                     intergenic         na              na   \n",
       "29                                     intergenic         na              na   \n",
       "..                                            ...        ...             ...   \n",
       "91                                  GUCY2GP;ACSL5         na              na   \n",
       "92                                     intergenic  HTMCP_307             YES   \n",
       "93                            MPPED2;ANKFN1;FGF12  HTMCP_309              NO   \n",
       "94                                         PTPN13  HTMCP_310             YES   \n",
       "95                               RASEF;intergenic         na              na   \n",
       "96                                     intergenic         na              na   \n",
       "97                                              -         na              na   \n",
       "98                                              -         na              na   \n",
       "99                                              -         na              na   \n",
       "100                                    intergenic         na              na   \n",
       "101                                    intergenic         na              na   \n",
       "102                                             -         na              na   \n",
       "103                           AK127472;intergenic  HTMCP_406             YES   \n",
       "104                                             -         na              na   \n",
       "105                                             -         na              na   \n",
       "106                                          IRS1         na              na   \n",
       "107                        COL4A5;intergenic;IRS4         na              na   \n",
       "108                                             -  HTMCP_409             YES   \n",
       "109                                             -         na              na   \n",
       "110                                             -         na              na   \n",
       "111                                             -         na              na   \n",
       "112                            CLPTM1L;intergenic         na              na   \n",
       "113                              intergenic;TUBD1         na              na   \n",
       "114                                            na  HTMCP_174             YES   \n",
       "115                                            na  HTMCP_230              NO   \n",
       "116                                            na  HTMCP_235             YES   \n",
       "117                                            na  HTMCP_249             YES   \n",
       "118                                            na  HTMCP_281              NO   \n",
       "119                                            na  HTMCP_281              NO   \n",
       "120                                            na  HTMCP_290             YES   \n",
       "\n",
       "                                  human-breakpoint_DNA  \\\n",
       "0                                                   na   \n",
       "1                                                   na   \n",
       "2                                                    -   \n",
       "3                                                   na   \n",
       "4                                                   na   \n",
       "5                                                   na   \n",
       "6                                                   na   \n",
       "7                                                   na   \n",
       "8                                                   na   \n",
       "9                                                    -   \n",
       "10                                                  na   \n",
       "11                                         17_36310359   \n",
       "12                                                  na   \n",
       "13                                                  na   \n",
       "14                                                  na   \n",
       "15                                                   -   \n",
       "16                                                   -   \n",
       "17                                                  na   \n",
       "18                             1_151029494;1_151029496   \n",
       "19                    19_1181971;19_1183502;19_1192727   \n",
       "20                                                  na   \n",
       "21                                                  na   \n",
       "22                                                   -   \n",
       "23                                                  na   \n",
       "24                 18_37408866;8_128319365;8_128323246   \n",
       "25                                                  na   \n",
       "26                 2_141933994;2_142008771;22_42896541   \n",
       "27                                                  na   \n",
       "28                                                  na   \n",
       "29                                                  na   \n",
       "..                                                 ...   \n",
       "91                                                  na   \n",
       "92                                         10_99063964   \n",
       "93                                                   -   \n",
       "94                               4_87540666;4_87644435   \n",
       "95                                                  na   \n",
       "96                                                  na   \n",
       "97                                                  na   \n",
       "98                                                  na   \n",
       "99                                                  na   \n",
       "100                                                 na   \n",
       "101                                                 na   \n",
       "102                                                 na   \n",
       "103                                        6_127148053   \n",
       "104                                                 na   \n",
       "105                                                 na   \n",
       "106                                                 na   \n",
       "107                                                 na   \n",
       "108  15_72233495;15_72236104;16_79363861;16_7942275...   \n",
       "109                                                 na   \n",
       "110                                                 na   \n",
       "111                                                 na   \n",
       "112                                                 na   \n",
       "113                                                 na   \n",
       "114                                        2_137648071   \n",
       "115                                                  -   \n",
       "116                                        8_128302005   \n",
       "117                                        18_28136581   \n",
       "118                                                  -   \n",
       "119                                                  -   \n",
       "120                                          6_3289268   \n",
       "\n",
       "                                   gene_DNA library_DNA  \n",
       "0                                        na          na  \n",
       "1                                        na          na  \n",
       "2                                         -      A37236  \n",
       "3                                        na          na  \n",
       "4                                        na          na  \n",
       "5                                        na          na  \n",
       "6                                        na          na  \n",
       "7                                        na          na  \n",
       "8                                        na          na  \n",
       "9                                         -      A37243  \n",
       "10                                       na          na  \n",
       "11                               intergenic      A37243  \n",
       "12                                       na          na  \n",
       "13                                       na          na  \n",
       "14                                       na          na  \n",
       "15                                        -      A37252  \n",
       "16                                        -      A37253  \n",
       "17                                       na          na  \n",
       "18                                 CDC42SE1      A37255  \n",
       "19                               intergenic      A37257  \n",
       "20                                       na          na  \n",
       "21                                       na          na  \n",
       "22                                        -      A37259  \n",
       "23                                       na          na  \n",
       "24   intergenic;DQ515899,DQ515898,LOC727677      A37261  \n",
       "25                                       na          na  \n",
       "26                         LRP1B;intergenic      A37266  \n",
       "27                                       na          na  \n",
       "28                                       na          na  \n",
       "29                                       na          na  \n",
       "..                                      ...         ...  \n",
       "91                                       na          na  \n",
       "92                               intergenic      A52339  \n",
       "93                                        -      A54387  \n",
       "94                                   PTPN13      A52340  \n",
       "95                                       na          na  \n",
       "96                                       na          na  \n",
       "97                                       na          na  \n",
       "98                                       na          na  \n",
       "99                                       na          na  \n",
       "100                                      na          na  \n",
       "101                                      na          na  \n",
       "102                                      na          na  \n",
       "103                                AK127472      A57091  \n",
       "104                                      na          na  \n",
       "105                                      na          na  \n",
       "106                                      na          na  \n",
       "107                                      na          na  \n",
       "108         MYO9A;intergenic;COL6A3;LRRFIP1      A57094  \n",
       "109                                      na          na  \n",
       "110                                      na          na  \n",
       "111                                      na          na  \n",
       "112                                      na          na  \n",
       "113                                      na          na  \n",
       "114                                  THSD7B      A37284  \n",
       "115                                       -      A38427  \n",
       "116             DQ515899,DQ515898,LOC727677      A38432  \n",
       "117                              intergenic      A38446  \n",
       "118                                       -      A52320  \n",
       "119                                       -      A52320  \n",
       "120       SLC22A23,CFB,TNXB,C4B_2,C2,HSPA1L      A54381  \n",
       "\n",
       "[121 rows x 11 columns]"
      ]
     },
     "execution_count": 428,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged = pd.merge(DNA_GRP, RNA_GRP, on=['patient', 'virus'], how='outer', suffixes=('_RNA', '_DNA'))\n",
    "merged.fillna('na', inplace=True)\n",
    "merged.to_csv('test_final_merged.csv', sep='\\t')\n",
    "merged"
   ]
  }
 ],
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