prepare_data_for_dnds_cv.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import argparse\n",
    "import os\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "import numpy\n",
    "\n",
    "from collections import Counter\n",
    "\n",
    "pathPrefix = '/Users/friedman/Desktop/mnt'\n",
    "\n",
    "sys.path.append(pathPrefix + '/ifs/work/taylorlab/friedman/myUtils')\n",
    "import analysis_utils \n",
    "import mutationSigUtils \n",
    "import maf_analysis_utils\n",
    "import clonality_analysis_util\n",
    "import re\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (17,18,19,45,46,48,50,51,52,53,54,55,56,57,60,61,62,63,64,65,74,75,76,77,78,80,81,85,86,87,89,90,91,92,93,98,100,101,102,103,104,105,106,107,108,110,111,112,113,114,115,116,117,121) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  interactivity=interactivity, compiler=compiler, result=result)\n"
     ]
    }
   ],
   "source": [
    "allImpactMutsUnfiltered = pd.read_table(pathPrefix + '/ifs/work/taylorlab/friedman/mskImpactAsOfMarch2019/dmp/mskimpact/data_mutations_unfiltered.txt', skiprows=[0])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "endometrialHyperIds = analysis_utils.get_ids_by_hypermutant_status(hypermutantIdDir=pathPrefix + '/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/hypermutationStatusIds', cancerType='Endometrial Cancer', hypermutantStatus = 'Hypermutated')\n",
    "colorectalHyperIds = analysis_utils.get_ids_by_hypermutant_status(hypermutantIdDir=pathPrefix +'/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/hypermutationStatusIds', cancerType='Colorectal Cancer', hypermutantStatus = 'Hypermutated')\n",
    "gliomaHyperIds = analysis_utils.get_ids_by_hypermutant_status(hypermutantIdDir=pathPrefix +'/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/hypermutationStatusIds', cancerType='Glioma', hypermutantStatus = 'Hypermutated')\n",
    "\n",
    "endometrialNormalIds = analysis_utils.get_ids_by_hypermutant_status(hypermutantIdDir=pathPrefix + '/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/hypermutationStatusIds', cancerType='Endometrial Cancer', hypermutantStatus = 'Normal')\n",
    "colorectalNormalIds = analysis_utils.get_ids_by_hypermutant_status(hypermutantIdDir=pathPrefix +'/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/hypermutationStatusIds', cancerType='Colorectal Cancer', hypermutantStatus = 'Normal')\n",
    "gliomaNormalIds = analysis_utils.get_ids_by_hypermutant_status(hypermutantIdDir=pathPrefix +'/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/hypermutationStatusIds', cancerType='Glioma', hypermutantStatus = 'Normal')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "endometrialHyperMuts = allImpactMutsUnfiltered[allImpactMutsUnfiltered['Tumor_Sample_Barcode'].isin(endometrialHyperIds)]\n",
    "colorectalHyperMuts = allImpactMutsUnfiltered[allImpactMutsUnfiltered['Tumor_Sample_Barcode'].isin(colorectalHyperIds)]\n",
    "gliomaHyperMuts = allImpactMutsUnfiltered[allImpactMutsUnfiltered['Tumor_Sample_Barcode'].isin(gliomaHyperIds)]\n",
    "\n",
    "endometrialNormalMuts = allImpactMutsUnfiltered[allImpactMutsUnfiltered['Tumor_Sample_Barcode'].isin(endometrialNormalIds)]\n",
    "colorectalNormalMuts = allImpactMutsUnfiltered[allImpactMutsUnfiltered['Tumor_Sample_Barcode'].isin(colorectalNormalIds)]\n",
    "gliomaNormalMuts = allImpactMutsUnfiltered[allImpactMutsUnfiltered['Tumor_Sample_Barcode'].isin(gliomaNormalIds)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "impactSigs = pd.read_table(pathPrefix + '/ifs/work/taylorlab/friedman/hypermutationAnalysisProj/projectDataAndConfigFiles/signatures_from_unfiltered_maf.txt')\n",
    "\n",
    "impactSigs = mutationSigUtils.merge_signature_columns(impactSigs)\n",
    "impactSigs['dominantSignature'] = impactSigs.apply(lambda row: \n",
    "        mutationSigUtils.get_dominant_signature(row.to_dict(), cols=None, prefix='mean', notEnoughMuts= True), axis=1)\n",
    "\n",
    "dominantSignaturesDict = dict(zip(impactSigs['Tumor_Sample_Barcode'], impactSigs['dominantSignature']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "poleCases = set(impactSigs[(impactSigs['dominantSignature'] == 'mean_10') & (impactSigs['Nmut_Mb'] > 30)]['Tumor_Sample_Barcode'])\n",
    "mmrCases = set(impactSigs[(impactSigs['dominantSignature'] == 'mean_MMR') & (impactSigs['Nmut_Mb'] > 30)]['Tumor_Sample_Barcode'])\n",
    "tmzCases = set(impactSigs[(impactSigs['dominantSignature'] == 'mean_11') & (impactSigs['Nmut_Mb'] > 30)]['Tumor_Sample_Barcode'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "poleMuts = endometrialMuts[endometrialMuts['Tumor_Sample_Barcode'].isin(poleCases)]\n",
    "mmrMuts = endometrialMuts[endometrialMuts['Tumor_Sample_Barcode'].isin(mmrCases)]\n",
    "tmzMuts = endometrialMuts[endometrialMuts['Tumor_Sample_Barcode'].isin(tmzCases)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "endometrialNormalMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/endometrialNormalMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "colorectalNormalMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/colorectalNormalMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "gliomaNormalMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/gliomaNormalMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "\n",
    "endometrialHyperMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/endometrialHypermutatedMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "colorectalHyperMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/colorectalHypermutatedMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "gliomaHyperMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/gliomaHypermutatedMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "\n",
    "poleMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/poleMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "mmrMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/mmrMutationsUnfiltered.maf', index=False, sep='\\t')\n",
    "tmzMuts.to_csv('/Users/friedman/Desktop/mnt/ifs/work/taylorlab/friedman/myAdjustedDataFiles/tmzMutationsUnfiltered.maf', index=False, sep='\\t')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**QC of DNDSCV outputs**<br><br><br><br>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "colorectalDndsCv = pd.read_table('/Users/friedman/Desktop/hypermutationAnalysisProj/colorectalCancerHyperDNDS.tsv')\n",
    "endometrialDndsCv = pd.read_table('/Users/friedman/Desktop/hypermutationAnalysisProj/endometrialCancerHyperDNDS.tsv')\n",
    "gliomaDndsCv = pd.read_table('/Users/friedman/Desktop/hypermutationAnalysisProj/gliomaHyperDNDS.tsv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "def qc_dnds_cv(dndsResults, maf):\n",
    "    indelGeneDict = dict(zip(dndsResults['gene_name'], dndsResults['n_ind']))\n",
    "    \n",
    "    for gene in set(dndsResults['gene_name']):\n",
    "        geneMaf = maf[maf['Hugo_Symbol'] == gene]\n",
    "        indelMaf = geneMaf[(geneMaf['Variant_Type'] == 'INS') | (geneMaf['Variant_Type'] == 'DEL')]\n",
    "        #nIndels = indelMaf.shape[0]\n",
    "        nIndels = len(set(indelMaf['HGVSp_Short']))\n",
    "\n",
    "        nIndelsDnds = indelGeneDict[gene]\n",
    "        print gene, nIndels - nIndelsDnds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py:3: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
      "  This is separate from the ipykernel package so we can avoid doing imports until\n"
     ]
    }
   ],
   "source": [
    "colorectalDndsCv['chrPosGene'] = colorectalDndsCv.apply(lambda row: str(row['chr']) + '_' + str(row['pos']) + '_' + row['gene'], axis=1)\n",
    "\n",
    "colorectalHyperMuts['chrPosGene'] = colorectalHyperMuts.apply(lambda row: str(row['Chromosome']) + '_' + str(row['Start_Position']) + '_' + str(row['Hugo_Symbol']), axis=1)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [],
   "source": [
    "def quantify_dnds_fuckup(gene, posDict, classDict):\n",
    "    DNDS = set(colorectalDndsCv[colorectalDndsCv['gene'] == gene]['chrPosGene'])\n",
    "    DNDScount = Counter(colorectalDndsCv[colorectalDndsCv['gene'] == gene]['chrPosGene'])\n",
    "    Obs = set(colorectalHyperMuts[colorectalHyperMuts['Hugo_Symbol'] == gene]['chrPosGene'])\n",
    "    Obscount = Counter(colorectalHyperMuts[colorectalHyperMuts['Hugo_Symbol'] == gene]['chrPosGene'])\n",
    "    missingVals = Obs - DNDS\n",
    "    absMissing = Obscount - DNDScount\n",
    "    \n",
    "    #print absMissing\n",
    "    \n",
    "    x = []\n",
    "    counts = []\n",
    "    for val in missingVals:\n",
    "        if val in posDict:\n",
    "            x.append(classDict[val])\n",
    "            counts.append((posDict[val], absMissing[val]))\n",
    "    \n",
    "    print Counter(counts)\n",
    "    print ''\n",
    "    print Counter(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [],
   "source": [
    "posDict = dict(zip(colorectalHyperMuts['chrPosGene'], colorectalHyperMuts['HGVSp_Short']))\n",
    "varClassDict = dict(zip(colorectalHyperMuts['chrPosGene'], colorectalHyperMuts['Variant_Classification']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "dfKras = pd.read_table('/Users/friedman/Desktop/hypermutationAnalysisProj/krasDNDS_test.tsv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "#for debug work with martincorena\n",
    "def check_inclusion(x):\n",
    "    if isinstance(x, basestring):\n",
    "        if 'p.' in x: return True\n",
    "        else: return False\n",
    "    else:\n",
    "        return False\n",
    "        \n",
    "dfKras['inclusion'] = dfKras['hgvs'].apply(lambda x: check_inclusion(x))\n",
    "dfKrasLim = dfKras[dfKras['inclusion'] == True]\n",
    "dfKrasLim.to_csv('~/Desktop/dndsCVBugTest.tsv', index=False, sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sampleID</th>\n",
       "      <th>chr</th>\n",
       "      <th>pos</th>\n",
       "      <th>ref</th>\n",
       "      <th>alt</th>\n",
       "      <th>gene</th>\n",
       "      <th>hgvs</th>\n",
       "      <th>inclusion</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>P-0039054-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25380283</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.A59T</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>P-0038520-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398281</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>P-0004379-T02-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25368397</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.I183N</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>P-0037690-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25380283</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.A59T</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>P-0033467-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398282</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13C</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>P-0033682-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25380275</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.Q61H</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>P-0033682-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398279</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.V14I</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>P-0035146-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25380283</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.A59T</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>P-0033583-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398281</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>P-0031059-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12V</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>P-0029121-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>P-0029337-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12V</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>P-0029683-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>P-0029778-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>P-0028144-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>P-0028034-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398281</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>P-0027698-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25368445</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.R167I</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>P-0016801-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12V</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>P-0018005-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>P-0019986-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398285</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12C</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>P-0025735-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398281</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>P-0009585-T01-IM5</td>\n",
       "      <td>12</td>\n",
       "      <td>25368476</td>\n",
       "      <td>A</td>\n",
       "      <td>-</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.Y157Ifs*4</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>P-0025003-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25380275</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.Q61H</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>P-0024733-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>P-0020509-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>P-0014495-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12V</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>P-0015048-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398220</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.D33E</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>P-0012740-T01-IM5</td>\n",
       "      <td>12</td>\n",
       "      <td>25398281</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>P-0012988-T01-IM5</td>\n",
       "      <td>12</td>\n",
       "      <td>25398281</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G13D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>P-0014388-T01-IM6</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>P-0009985-T01-IM5</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12D</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>P-0001248-T01-IM3</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12V</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>P-0005285-T01-IM5</td>\n",
       "      <td>12</td>\n",
       "      <td>25398284</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.G12A</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>P-0004379-T01-IM5</td>\n",
       "      <td>12</td>\n",
       "      <td>25368397</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>KRAS</td>\n",
       "      <td>p.I183N</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             sampleID  chr       pos ref alt  gene         hgvs  inclusion\n",
       "1   P-0039054-T01-IM6   12  25380283   C   T  KRAS       p.A59T       True\n",
       "3   P-0038520-T01-IM6   12  25398281   C   T  KRAS       p.G13D       True\n",
       "5   P-0004379-T02-IM6   12  25368397   A   T  KRAS      p.I183N       True\n",
       "6   P-0037690-T01-IM6   12  25380283   C   T  KRAS       p.A59T       True\n",
       "7   P-0033467-T01-IM6   12  25398282   C   A  KRAS       p.G13C       True\n",
       "8   P-0033682-T01-IM6   12  25380275   T   G  KRAS       p.Q61H       True\n",
       "9   P-0033682-T01-IM6   12  25398279   C   T  KRAS       p.V14I       True\n",
       "11  P-0035146-T01-IM6   12  25380283   C   T  KRAS       p.A59T       True\n",
       "13  P-0033583-T01-IM6   12  25398281   C   T  KRAS       p.G13D       True\n",
       "14  P-0031059-T01-IM6   12  25398284   C   A  KRAS       p.G12V       True\n",
       "15  P-0029121-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "16  P-0029337-T01-IM6   12  25398284   C   A  KRAS       p.G12V       True\n",
       "17  P-0029683-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "19  P-0029778-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "22  P-0028144-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "23  P-0028034-T01-IM6   12  25398281   C   T  KRAS       p.G13D       True\n",
       "24  P-0027698-T01-IM6   12  25368445   C   A  KRAS      p.R167I       True\n",
       "26  P-0016801-T01-IM6   12  25398284   C   A  KRAS       p.G12V       True\n",
       "28  P-0018005-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "29  P-0019986-T01-IM6   12  25398285   C   A  KRAS       p.G12C       True\n",
       "30  P-0025735-T01-IM6   12  25398281   C   T  KRAS       p.G13D       True\n",
       "32  P-0009585-T01-IM5   12  25368476   A   -  KRAS  p.Y157Ifs*4       True\n",
       "33  P-0025003-T01-IM6   12  25380275   T   G  KRAS       p.Q61H       True\n",
       "34  P-0024733-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "36  P-0020509-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "37  P-0014495-T01-IM6   12  25398284   C   A  KRAS       p.G12V       True\n",
       "38  P-0015048-T01-IM6   12  25398220   A   C  KRAS       p.D33E       True\n",
       "39  P-0012740-T01-IM5   12  25398281   C   T  KRAS       p.G13D       True\n",
       "42  P-0012988-T01-IM5   12  25398281   C   T  KRAS       p.G13D       True\n",
       "43  P-0014388-T01-IM6   12  25398284   C   T  KRAS       p.G12D       True\n",
       "44  P-0009985-T01-IM5   12  25398284   C   T  KRAS       p.G12D       True\n",
       "46  P-0001248-T01-IM3   12  25398284   C   A  KRAS       p.G12V       True\n",
       "47  P-0005285-T01-IM5   12  25398284   C   G  KRAS       p.G12A       True\n",
       "48  P-0004379-T01-IM5   12  25368397   A   T  KRAS      p.I183N       True"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dfKrasLim"
   ]
  }
 ],
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