GSE178265_xml_parse.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import xml.etree.ElementTree as ET\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def parse_attributes(attributes):\n",
    "    \n",
    "    # create dictionary for attribute value\n",
    "    attribute_data = {}\n",
    "    \n",
    "    for attribute in attributes.findall('Attribute'):\n",
    "        attribute_name = attribute.get('attribute_name')\n",
    "        attribute_value = attribute.text\n",
    "        attribute_data[attribute_name] = attribute_value\n",
    "    return attribute_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# define function for child node \n",
    "def parse_biosample(biosample):\n",
    "    \n",
    "    # create dictionary for biosample value\n",
    "    biosample_data = {}\n",
    "    \n",
    "    biosample_data['ID'] = biosample.get('accession')\n",
    "    biosample_data['Title'] = biosample.find('Description/Title').text\n",
    "    biosample_data['OrganismName'] = biosample.find('Description/Organism/OrganismName').text\n",
    "    owner = biosample.find('Owner')\n",
    "    biosample_data['OwnerName'] = owner.find('Name').text\n",
    "    biosample_data['OwnerEmail'] = owner.find('Contacts/Contact').get('email')\n",
    "    biosample_data['Model'] = biosample.find('Models/Model').text\n",
    "    biosample_data['Package'] = biosample.find('Package').get('display_name')\n",
    "    status = biosample.find('Status')\n",
    "    biosample_data['Status'] = status.get('status') if status is not None else None\n",
    "    attributes = biosample.find('Attributes')\n",
    "    \n",
    "    \n",
    "    if attributes is not None:\n",
    "        attribute_data = parse_attributes(attributes)\n",
    "        biosample_data.update(attribute_data)   #using .update to add data \n",
    "    return biosample_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "\n",
    "def xml_to_dataframe(xml_file):\n",
    "    tree = ET.parse(xml_file)\n",
    "    root = tree.getroot()\n",
    "    \n",
    "    \n",
    "    # create empty list to append\n",
    "    biosample_data_list = []\n",
    "    \n",
    "    # similar to for i in root.findall()\n",
    "    for biosample in root.findall('BioSample'):\n",
    "        biosample_data = parse_biosample(biosample)\n",
    "        biosample_data_list.append(biosample_data)\n",
    "    df = pd.DataFrame(biosample_data_list)\n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "               ID                        Title  OrganismName        OwnerName  \\\n",
      "0    SAMN19715322   pPDsHSrSNxi3322d200429PosH  Homo sapiens  Broad Institute   \n",
      "1    SAMN19715320   pPDsHSrSNxi2544d200429PosA  Homo sapiens  Broad Institute   \n",
      "2    SAMN19715318   pPDsHSrSNxi2544d200429PosC  Homo sapiens  Broad Institute   \n",
      "3    SAMN19715316  pPDsHSrSNxi3322d200429DAPIC  Homo sapiens  Broad Institute   \n",
      "4    SAMN19715315   pPDsHSrSNxi2569d200429PosA  Homo sapiens  Broad Institute   \n",
      "..            ...                          ...           ...              ...   \n",
      "96   SAMN19715165  pPDsHSrSNxi3482d200429DAPIB  Homo sapiens  Broad Institute   \n",
      "97   SAMN19715164   pPDsHSrSNxi4956d200429PosA  Homo sapiens  Broad Institute   \n",
      "98   SAMN19715163  pPDsHSrSNxi3482d200429DAPIA  Homo sapiens  Broad Institute   \n",
      "99   SAMN19715162   pPDsHSrSNxi3322d200429PosF  Homo sapiens  Broad Institute   \n",
      "100  SAMN19715161  pPDsHSrSNxi6173d200429DAPIA  Homo sapiens  Broad Institute   \n",
      "\n",
      "                      OwnerEmail    Model  Package Status  \\\n",
      "0    emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "1    emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "2    emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "3    emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "4    emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "..                           ...      ...      ...    ...   \n",
      "96   emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "97   emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "98   emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "99   emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "100  emacosko@broadinstitute.org  Generic  Generic   live   \n",
      "\n",
      "                              source_name                          tissue  \\\n",
      "0    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "1    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "2    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "3    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "4    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "..                                    ...                             ...   \n",
      "96   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "97   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "98   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "99   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "100  Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
      "\n",
      "        Sex age   pmi  disease status           Cause of death  \\\n",
      "0    female  90    22     Ctrl   Ctrl             Colon cancer   \n",
      "1    female  89    10  Disease    LBD       Lewy body dementia   \n",
      "2    female  89    10  Disease    LBD       Lewy body dementia   \n",
      "3    female  90    22     Ctrl   Ctrl             Colon cancer   \n",
      "4      male  74    13  Disease    LBD       Lewy body dementia   \n",
      "..      ...  ..   ...      ...    ...                      ...   \n",
      "96   female  79    14     Ctrl   Ctrl  Coronary artery disease   \n",
      "97   female  92  23.3     Ctrl   Ctrl          Prostate cancer   \n",
      "98   female  79    14     Ctrl   Ctrl  Coronary artery disease   \n",
      "99   female  90    22     Ctrl   Ctrl             Colon cancer   \n",
      "100    male  49   7.2     Ctrl   Ctrl               Not listed   \n",
      "\n",
      "    facs classification 10x version genome build  \n",
      "0              Positive          V3         hg19  \n",
      "1              Positive          V3         hg19  \n",
      "2              Positive          V3         hg19  \n",
      "3              Negative          V3         hg19  \n",
      "4              Positive          V3         hg19  \n",
      "..                  ...         ...          ...  \n",
      "96             Negative          V3         hg19  \n",
      "97             Positive          V3         hg19  \n",
      "98             Negative          V3         hg19  \n",
      "99             Positive          V3         hg19  \n",
      "100            Negative          V3         hg19  \n",
      "\n",
      "[101 rows x 19 columns]\n"
     ]
    }
   ],
   "source": [
    "xml_file_path = '/home/supakorn/biosample_result.xml'\n",
    "df = xml_to_dataframe(xml_file_path)\n",
    "print(df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "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>ID</th>\n",
       "      <th>Title</th>\n",
       "      <th>OrganismName</th>\n",
       "      <th>OwnerName</th>\n",
       "      <th>OwnerEmail</th>\n",
       "      <th>Model</th>\n",
       "      <th>Package</th>\n",
       "      <th>Status</th>\n",
       "      <th>source_name</th>\n",
       "      <th>tissue</th>\n",
       "      <th>Sex</th>\n",
       "      <th>age</th>\n",
       "      <th>pmi</th>\n",
       "      <th>disease</th>\n",
       "      <th>status</th>\n",
       "      <th>Cause of death</th>\n",
       "      <th>facs classification</th>\n",
       "      <th>10x version</th>\n",
       "      <th>genome build</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SAMN19715322</td>\n",
       "      <td>pPDsHSrSNxi3322d200429PosH</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>90</td>\n",
       "      <td>22</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Colon cancer</td>\n",
       "      <td>Positive</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SAMN19715320</td>\n",
       "      <td>pPDsHSrSNxi2544d200429PosA</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>89</td>\n",
       "      <td>10</td>\n",
       "      <td>Disease</td>\n",
       "      <td>LBD</td>\n",
       "      <td>Lewy body dementia</td>\n",
       "      <td>Positive</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SAMN19715318</td>\n",
       "      <td>pPDsHSrSNxi2544d200429PosC</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>89</td>\n",
       "      <td>10</td>\n",
       "      <td>Disease</td>\n",
       "      <td>LBD</td>\n",
       "      <td>Lewy body dementia</td>\n",
       "      <td>Positive</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SAMN19715316</td>\n",
       "      <td>pPDsHSrSNxi3322d200429DAPIC</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>90</td>\n",
       "      <td>22</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Colon cancer</td>\n",
       "      <td>Negative</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SAMN19715315</td>\n",
       "      <td>pPDsHSrSNxi2569d200429PosA</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>male</td>\n",
       "      <td>74</td>\n",
       "      <td>13</td>\n",
       "      <td>Disease</td>\n",
       "      <td>LBD</td>\n",
       "      <td>Lewy body dementia</td>\n",
       "      <td>Positive</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</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",
       "      <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>96</th>\n",
       "      <td>SAMN19715165</td>\n",
       "      <td>pPDsHSrSNxi3482d200429DAPIB</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>79</td>\n",
       "      <td>14</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Coronary artery disease</td>\n",
       "      <td>Negative</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>SAMN19715164</td>\n",
       "      <td>pPDsHSrSNxi4956d200429PosA</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>92</td>\n",
       "      <td>23.3</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Prostate cancer</td>\n",
       "      <td>Positive</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>SAMN19715163</td>\n",
       "      <td>pPDsHSrSNxi3482d200429DAPIA</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>79</td>\n",
       "      <td>14</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Coronary artery disease</td>\n",
       "      <td>Negative</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99</th>\n",
       "      <td>SAMN19715162</td>\n",
       "      <td>pPDsHSrSNxi3322d200429PosF</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>female</td>\n",
       "      <td>90</td>\n",
       "      <td>22</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Colon cancer</td>\n",
       "      <td>Positive</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>100</th>\n",
       "      <td>SAMN19715161</td>\n",
       "      <td>pPDsHSrSNxi6173d200429DAPIA</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Broad Institute</td>\n",
       "      <td>emacosko@broadinstitute.org</td>\n",
       "      <td>Generic</td>\n",
       "      <td>Generic</td>\n",
       "      <td>live</td>\n",
       "      <td>Human Substantia nigra pars compacta</td>\n",
       "      <td>Substantia nigra pars compacta</td>\n",
       "      <td>male</td>\n",
       "      <td>49</td>\n",
       "      <td>7.2</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Ctrl</td>\n",
       "      <td>Not listed</td>\n",
       "      <td>Negative</td>\n",
       "      <td>V3</td>\n",
       "      <td>hg19</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>101 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               ID                        Title  OrganismName        OwnerName  \\\n",
       "0    SAMN19715322   pPDsHSrSNxi3322d200429PosH  Homo sapiens  Broad Institute   \n",
       "1    SAMN19715320   pPDsHSrSNxi2544d200429PosA  Homo sapiens  Broad Institute   \n",
       "2    SAMN19715318   pPDsHSrSNxi2544d200429PosC  Homo sapiens  Broad Institute   \n",
       "3    SAMN19715316  pPDsHSrSNxi3322d200429DAPIC  Homo sapiens  Broad Institute   \n",
       "4    SAMN19715315   pPDsHSrSNxi2569d200429PosA  Homo sapiens  Broad Institute   \n",
       "..            ...                          ...           ...              ...   \n",
       "96   SAMN19715165  pPDsHSrSNxi3482d200429DAPIB  Homo sapiens  Broad Institute   \n",
       "97   SAMN19715164   pPDsHSrSNxi4956d200429PosA  Homo sapiens  Broad Institute   \n",
       "98   SAMN19715163  pPDsHSrSNxi3482d200429DAPIA  Homo sapiens  Broad Institute   \n",
       "99   SAMN19715162   pPDsHSrSNxi3322d200429PosF  Homo sapiens  Broad Institute   \n",
       "100  SAMN19715161  pPDsHSrSNxi6173d200429DAPIA  Homo sapiens  Broad Institute   \n",
       "\n",
       "                      OwnerEmail    Model  Package Status  \\\n",
       "0    emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "1    emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "2    emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "3    emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "4    emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "..                           ...      ...      ...    ...   \n",
       "96   emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "97   emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "98   emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "99   emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "100  emacosko@broadinstitute.org  Generic  Generic   live   \n",
       "\n",
       "                              source_name                          tissue  \\\n",
       "0    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "1    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "2    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "3    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "4    Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "..                                    ...                             ...   \n",
       "96   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "97   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "98   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "99   Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "100  Human Substantia nigra pars compacta  Substantia nigra pars compacta   \n",
       "\n",
       "        Sex age   pmi  disease status           Cause of death  \\\n",
       "0    female  90    22     Ctrl   Ctrl             Colon cancer   \n",
       "1    female  89    10  Disease    LBD       Lewy body dementia   \n",
       "2    female  89    10  Disease    LBD       Lewy body dementia   \n",
       "3    female  90    22     Ctrl   Ctrl             Colon cancer   \n",
       "4      male  74    13  Disease    LBD       Lewy body dementia   \n",
       "..      ...  ..   ...      ...    ...                      ...   \n",
       "96   female  79    14     Ctrl   Ctrl  Coronary artery disease   \n",
       "97   female  92  23.3     Ctrl   Ctrl          Prostate cancer   \n",
       "98   female  79    14     Ctrl   Ctrl  Coronary artery disease   \n",
       "99   female  90    22     Ctrl   Ctrl             Colon cancer   \n",
       "100    male  49   7.2     Ctrl   Ctrl               Not listed   \n",
       "\n",
       "    facs classification 10x version genome build  \n",
       "0              Positive          V3         hg19  \n",
       "1              Positive          V3         hg19  \n",
       "2              Positive          V3         hg19  \n",
       "3              Negative          V3         hg19  \n",
       "4              Positive          V3         hg19  \n",
       "..                  ...         ...          ...  \n",
       "96             Negative          V3         hg19  \n",
       "97             Positive          V3         hg19  \n",
       "98             Negative          V3         hg19  \n",
       "99             Positive          V3         hg19  \n",
       "100            Negative          V3         hg19  \n",
       "\n",
       "[101 rows x 19 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  }
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