awg_compare.ipynb

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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import synapseclient\n",
      "import subprocess\n",
      "from glob import glob\n",
      "import csv\n",
      "import gzip\n",
      "import pandas"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "syn = synapseclient.Synapse()\n",
      "syn.login()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Welcome, Kyle Ellrott!\n",
        "\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "\n",
        "UPGRADE AVAILABLE\n",
        "\n",
        "A more recent version of the Synapse Client (1.7.2) is available. Your version (1.5.1) can be upgraded by typing:\n",
        "    pip install --upgrade synapseclient\n",
        "\n",
        "Python Synapse Client version 1.7.2 release notes\n",
        "\n",
        "https://github.com/Sage-Bionetworks/synapsePythonClient/blob/master/release_notes/release-1.7.1.md\n",
        "\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "s = syn.get(\"syn1710680\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "subprocess.check_call(\"tar xvzf %s\" % (s.path), cwd=\"./Data\", shell=True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 4,
       "text": [
        "0"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "projects = list( a.split(\"/\")[2].replace(\"_cleaned.maf\", \"\") for a in glob(\"Data/somatic_mafs_cleaned/*.maf\") )"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def row_id(row):\n",
      "    return \"%s:%s:%s:%s\" % (row['Tumor_Sample_Barcode'], \n",
      "                            row['Chromosome'], \n",
      "                            row['Start_Position'],\n",
      "                            row['End_Position'])\n",
      "\n",
      "def row_extract(row):\n",
      "    out = {}\n",
      "    for i in [\"FILTER\", 'Variant_Type', 'CENTERS', \"mutval_status_targeted\",\n",
      "    \"mutval_status_wxs\", \"mutval_status_wgs\", \"mutval_status_rna\", \"mutval_status_lowpass\"]:\n",
      "        if i in row:\n",
      "            out[i] = row[i]\n",
      "    return out\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "awg_calls = {}\n",
      "for c in projects:\n",
      "    awg_calls[c] = {}\n",
      "    with open(\"Data/somatic_mafs_cleaned/%s_cleaned.maf\" % (c)) as handle:\n",
      "        reader = csv.DictReader(handle, delimiter=\"\\t\")\n",
      "        for row in reader:\n",
      "            if row['Variant_Type'] == \"SNP\":\n",
      "                sample = row['Tumor_Sample_Barcode']\n",
      "                if sample not in awg_calls[c]:\n",
      "                    awg_calls[c][sample] = {}\n",
      "                awg_calls[c][sample][ row_id(row) ] = row_extract(row)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "validation_file = \"Data/mc3_all_pairsets.aggregated.maf\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "validation_calls = {}\n",
      "with open(validation_file) as handle:\n",
      "    reader = csv.DictReader(handle, delimiter=\"\\t\")\n",
      "    for row in reader:\n",
      "        if row['Variant_Type'] == \"SNP\":\n",
      "            sample = row['Tumor_Sample_Barcode']\n",
      "            for proj in awg_calls:\n",
      "                if sample in awg_calls[proj]:\n",
      "                    if proj not in validation_calls:\n",
      "                        validation_calls[proj] = {}\n",
      "                    if sample not in validation_calls[proj]:\n",
      "                        validation_calls[proj][sample] = {}\n",
      "                    validation_calls[proj][sample][ row_id(row) ] = row_extract(row)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "public_file = \"Data/mc3.v0.2.8.PUBLIC.maf.gz\"\n",
      "public_calls = {}\n",
      "with gzip.GzipFile(public_file) as handle:\n",
      "    reader = csv.DictReader(handle, delimiter=\"\\t\")\n",
      "    for row in reader:\n",
      "        if row['Variant_Type'] == \"SNP\":\n",
      "            sample = row['Tumor_Sample_Barcode']\n",
      "            for proj in awg_calls:\n",
      "                if proj not in public_calls:\n",
      "                    public_calls[proj] = {}\n",
      "                if sample in awg_calls[proj]:\n",
      "                    if sample not in public_calls[proj]:\n",
      "                        public_calls[proj][sample] = {}\n",
      "                    public_calls[proj][sample][ row_id(row) ] = row_extract(row)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print len(validation_calls)\n",
      "\n",
      "val_order = [\n",
      "    \"mutval_status_targeted\",\n",
      "    \"mutval_status_wgs\",\n",
      "    #\"mutval_status_rna\",\n",
      "    #\"mutval_status_lowpass\"\n",
      "]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "18\n"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print awg_calls.keys()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "['stad', 'cesc', 'lusc', 'paad', 'coadread', 'kirp', 'gbm', 'lgg', 'laml', 'luad', 'thca', 'blca', 'ucec', 'prad', 'skcm', 'kirc', 'brca', 'ov', 'hnsc', 'pancan12']\n"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sum(len(a) for a in awg_calls['stad'].values() )"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 13,
       "text": [
        "83080"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "out = {}\n",
      "for proj in public_calls:\n",
      "    awg_counts = {}\n",
      "    val_counts = {}\n",
      "    pub_counts = {}\n",
      "    isect_counts = {}\n",
      "    if proj in validation_calls:\n",
      "        for sample in validation_calls[proj]:\n",
      "            if sample in public_calls[proj]:\n",
      "                for variant in validation_calls[proj][sample]:\n",
      "                    status = \"\"\n",
      "                    for v in val_order:\n",
      "                        if validation_calls[proj][sample][variant][v].endswith(\"_powered\"):\n",
      "                            status = validation_calls[proj][sample][variant][v]\n",
      "                            break\n",
      "                    if status != \"\":\n",
      "                        if variant in public_calls[proj][sample] and public_calls[proj][sample][variant]['FILTER'] == \"PASS\":\n",
      "                            if variant in awg_calls[proj][sample]:\n",
      "                                isect_counts[status] = isect_counts.get(status, 0) + 1\n",
      "                            else:\n",
      "                                pub_counts[status] = pub_counts.get(status, 0) + 1\n",
      "                        elif variant in awg_calls[proj][sample]:\n",
      "                            awg_counts[status] = awg_counts.get(status, 0) + 1\n",
      "                    \n",
      "    public_count = 0\n",
      "    isect_count = 0\n",
      "    awg_count = 0\n",
      "    public_unique_count = 0\n",
      "    awg_unique_count = 0\n",
      "    for sample in public_calls[proj]:\n",
      "        if sample in awg_calls[proj]:\n",
      "            for variant in public_calls[proj][sample]:\n",
      "                #if public_calls[proj][sample][variant][\"FILTER\"] == \"PASS\":\n",
      "                    public_count += 1\n",
      "                    if variant in awg_calls[proj][sample]:\n",
      "                        isect_count += 1\n",
      "                    else:\n",
      "                        public_unique_count += 1\n",
      "            for variant in awg_calls[proj][sample]:\n",
      "                awg_count += 1\n",
      "                if variant not in public_calls[proj][sample]:\n",
      "                    awg_unique_count += 1\n",
      "                \n",
      "            #awg_count += len(awg_calls[proj][sample])\n",
      "    row = {\"isec_samples\" : len(public_calls[proj]), \n",
      "           \"mc3_variant_count\" : public_count, \n",
      "           \"awg_variant_count\" : awg_count,\n",
      "           \"isec_variant_count\" :  isect_count,\n",
      "           \"mc3_variant_uniq_count\" : public_unique_count,\n",
      "           \"awg_variant_uniq_count\" : awg_unique_count,\n",
      "           \"coverage\" : float(isect_count) / float(awg_count),\n",
      "           \"isec_variant_validated\" : isect_counts.get(\"validated_powered\", 0),\n",
      "           \"isec_variant_unvalidated\" : isect_counts.get(\"unvalidated_powered\", 0),\n",
      "           \"mc3_variant_validated\" : pub_counts.get(\"validated_powered\", 0),\n",
      "           \"mc3_variant_unvalidated\" : pub_counts.get(\"unvalidated_powered\", 0),\n",
      "           \"awg_variant_validated\" : awg_counts.get(\"validated_powered\", 0),\n",
      "           \"awg_variant_unvalidated\" : awg_counts.get(\"unvalidated_powered\", 0)\n",
      "    }\n",
      "    out[proj] = row\n",
      "    \"\"\"\n",
      "    print proj\n",
      "    print awg_counts\n",
      "    print val_counts\n",
      "    print \"awg\", awg_count\n",
      "    print \"isect\", isect_count\n",
      "    print \"coverage\", float(isect_count) / float(awg_count)\n",
      "    if 'unvalidated_powered' in awg_counts and 'unvalidated_powered' in awg_counts:\n",
      "        print float(awg_counts['unvalidated_powered']) / (awg_counts['validated_powered'] + awg_counts['unvalidated_powered'])\n",
      "    if 'unvalidated_powered' in val_counts and 'unvalidated_powered' in val_counts:\n",
      "        print float(val_counts['unvalidated_powered']) / (val_counts['validated_powered'] + val_counts['unvalidated_powered'])\n",
      "    \"\"\" \n",
      "df = pandas.DataFrame(out).transpose()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 34
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "df.sort_values(\"coverage\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "<div style=\"max-width:1500px;overflow:auto;\">\n",
        "<table border=\"1\" class=\"dataframe\">\n",
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>awg_variant_count</th>\n",
        "      <th>awg_variant_uniq_count</th>\n",
        "      <th>awg_variant_unvalidated</th>\n",
        "      <th>awg_variant_validated</th>\n",
        "      <th>coverage</th>\n",
        "      <th>isec_samples</th>\n",
        "      <th>isec_variant_count</th>\n",
        "      <th>isec_variant_unvalidated</th>\n",
        "      <th>isec_variant_validated</th>\n",
        "      <th>mc3_variant_count</th>\n",
        "      <th>mc3_variant_uniq_count</th>\n",
        "      <th>mc3_variant_unvalidated</th>\n",
        "      <th>mc3_variant_validated</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>paad</th>\n",
        "      <td>3327.0</td>\n",
        "      <td>2218.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.333333</td>\n",
        "      <td>26.0</td>\n",
        "      <td>1109.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>1317.0</td>\n",
        "      <td>208.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>laml</th>\n",
        "      <td>1396.0</td>\n",
        "      <td>688.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.507163</td>\n",
        "      <td>127.0</td>\n",
        "      <td>708.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>5322.0</td>\n",
        "      <td>4614.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>prad</th>\n",
        "      <td>5331.0</td>\n",
        "      <td>2477.0</td>\n",
        "      <td>5.0</td>\n",
        "      <td>23.0</td>\n",
        "      <td>0.535359</td>\n",
        "      <td>82.0</td>\n",
        "      <td>2854.0</td>\n",
        "      <td>5.0</td>\n",
        "      <td>98.0</td>\n",
        "      <td>3436.0</td>\n",
        "      <td>582.0</td>\n",
        "      <td>4.0</td>\n",
        "      <td>20.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>thca</th>\n",
        "      <td>6725.0</td>\n",
        "      <td>2723.0</td>\n",
        "      <td>22.0</td>\n",
        "      <td>44.0</td>\n",
        "      <td>0.595093</td>\n",
        "      <td>321.0</td>\n",
        "      <td>4002.0</td>\n",
        "      <td>20.0</td>\n",
        "      <td>769.0</td>\n",
        "      <td>8338.0</td>\n",
        "      <td>4336.0</td>\n",
        "      <td>16.0</td>\n",
        "      <td>77.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>luad</th>\n",
        "      <td>78158.0</td>\n",
        "      <td>20771.0</td>\n",
        "      <td>220.0</td>\n",
        "      <td>1546.0</td>\n",
        "      <td>0.734243</td>\n",
        "      <td>192.0</td>\n",
        "      <td>57387.0</td>\n",
        "      <td>65.0</td>\n",
        "      <td>12625.0</td>\n",
        "      <td>70289.0</td>\n",
        "      <td>12902.0</td>\n",
        "      <td>23.0</td>\n",
        "      <td>2133.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>cesc</th>\n",
        "      <td>8979.0</td>\n",
        "      <td>1979.0</td>\n",
        "      <td>25.0</td>\n",
        "      <td>68.0</td>\n",
        "      <td>0.779597</td>\n",
        "      <td>39.0</td>\n",
        "      <td>7000.0</td>\n",
        "      <td>10.0</td>\n",
        "      <td>3300.0</td>\n",
        "      <td>8191.0</td>\n",
        "      <td>1191.0</td>\n",
        "      <td>10.0</td>\n",
        "      <td>297.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>gbm</th>\n",
        "      <td>17727.0</td>\n",
        "      <td>3067.0</td>\n",
        "      <td>4.0</td>\n",
        "      <td>410.0</td>\n",
        "      <td>0.826987</td>\n",
        "      <td>250.0</td>\n",
        "      <td>14660.0</td>\n",
        "      <td>6.0</td>\n",
        "      <td>1715.0</td>\n",
        "      <td>18231.0</td>\n",
        "      <td>3571.0</td>\n",
        "      <td>7.0</td>\n",
        "      <td>210.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>kirp</th>\n",
        "      <td>6074.0</td>\n",
        "      <td>919.0</td>\n",
        "      <td>19.0</td>\n",
        "      <td>24.0</td>\n",
        "      <td>0.848699</td>\n",
        "      <td>96.0</td>\n",
        "      <td>5155.0</td>\n",
        "      <td>6.0</td>\n",
        "      <td>579.0</td>\n",
        "      <td>13183.0</td>\n",
        "      <td>8028.0</td>\n",
        "      <td>3.0</td>\n",
        "      <td>80.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>lgg</th>\n",
        "      <td>23041.0</td>\n",
        "      <td>3115.0</td>\n",
        "      <td>13.0</td>\n",
        "      <td>32.0</td>\n",
        "      <td>0.864806</td>\n",
        "      <td>170.0</td>\n",
        "      <td>19926.0</td>\n",
        "      <td>11.0</td>\n",
        "      <td>1103.0</td>\n",
        "      <td>23659.0</td>\n",
        "      <td>3733.0</td>\n",
        "      <td>15.0</td>\n",
        "      <td>104.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>stad</th>\n",
        "      <td>63600.0</td>\n",
        "      <td>8260.0</td>\n",
        "      <td>123.0</td>\n",
        "      <td>2362.0</td>\n",
        "      <td>0.870126</td>\n",
        "      <td>112.0</td>\n",
        "      <td>55340.0</td>\n",
        "      <td>33.0</td>\n",
        "      <td>6497.0</td>\n",
        "      <td>62345.0</td>\n",
        "      <td>7005.0</td>\n",
        "      <td>7.0</td>\n",
        "      <td>822.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>kirc</th>\n",
        "      <td>15894.0</td>\n",
        "      <td>1995.0</td>\n",
        "      <td>7.0</td>\n",
        "      <td>34.0</td>\n",
        "      <td>0.874481</td>\n",
        "      <td>245.0</td>\n",
        "      <td>13899.0</td>\n",
        "      <td>5.0</td>\n",
        "      <td>1299.0</td>\n",
        "      <td>17310.0</td>\n",
        "      <td>3411.0</td>\n",
        "      <td>8.0</td>\n",
        "      <td>141.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>ov</th>\n",
        "      <td>10140.0</td>\n",
        "      <td>1257.0</td>\n",
        "      <td>9.0</td>\n",
        "      <td>474.0</td>\n",
        "      <td>0.876036</td>\n",
        "      <td>168.0</td>\n",
        "      <td>8883.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>18547.0</td>\n",
        "      <td>9664.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>lusc</th>\n",
        "      <td>62860.0</td>\n",
        "      <td>6626.0</td>\n",
        "      <td>56.0</td>\n",
        "      <td>754.0</td>\n",
        "      <td>0.894591</td>\n",
        "      <td>173.0</td>\n",
        "      <td>56234.0</td>\n",
        "      <td>32.0</td>\n",
        "      <td>10225.0</td>\n",
        "      <td>73201.0</td>\n",
        "      <td>16967.0</td>\n",
        "      <td>11.0</td>\n",
        "      <td>1839.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>pancan12</th>\n",
        "      <td>512835.0</td>\n",
        "      <td>51087.0</td>\n",
        "      <td>520.0</td>\n",
        "      <td>41079.0</td>\n",
        "      <td>0.900383</td>\n",
        "      <td>2652.0</td>\n",
        "      <td>461748.0</td>\n",
        "      <td>230.0</td>\n",
        "      <td>64912.0</td>\n",
        "      <td>636448.0</td>\n",
        "      <td>174700.0</td>\n",
        "      <td>164.0</td>\n",
        "      <td>10313.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>hnsc</th>\n",
        "      <td>52688.0</td>\n",
        "      <td>4541.0</td>\n",
        "      <td>36.0</td>\n",
        "      <td>1643.0</td>\n",
        "      <td>0.913813</td>\n",
        "      <td>289.0</td>\n",
        "      <td>48147.0</td>\n",
        "      <td>28.0</td>\n",
        "      <td>5970.0</td>\n",
        "      <td>62316.0</td>\n",
        "      <td>14169.0</td>\n",
        "      <td>17.0</td>\n",
        "      <td>879.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>skcm</th>\n",
        "      <td>174659.0</td>\n",
        "      <td>14467.0</td>\n",
        "      <td>27.0</td>\n",
        "      <td>665.0</td>\n",
        "      <td>0.917170</td>\n",
        "      <td>248.0</td>\n",
        "      <td>160192.0</td>\n",
        "      <td>35.0</td>\n",
        "      <td>28367.0</td>\n",
        "      <td>322299.0</td>\n",
        "      <td>162107.0</td>\n",
        "      <td>31.0</td>\n",
        "      <td>6185.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>brca</th>\n",
        "      <td>40439.0</td>\n",
        "      <td>3296.0</td>\n",
        "      <td>29.0</td>\n",
        "      <td>5316.0</td>\n",
        "      <td>0.918495</td>\n",
        "      <td>760.0</td>\n",
        "      <td>37143.0</td>\n",
        "      <td>10.0</td>\n",
        "      <td>5900.0</td>\n",
        "      <td>61727.0</td>\n",
        "      <td>24584.0</td>\n",
        "      <td>29.0</td>\n",
        "      <td>1269.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>blca</th>\n",
        "      <td>28165.0</td>\n",
        "      <td>1997.0</td>\n",
        "      <td>12.0</td>\n",
        "      <td>246.0</td>\n",
        "      <td>0.929096</td>\n",
        "      <td>95.0</td>\n",
        "      <td>26168.0</td>\n",
        "      <td>21.0</td>\n",
        "      <td>4417.0</td>\n",
        "      <td>32769.0</td>\n",
        "      <td>6601.0</td>\n",
        "      <td>3.0</td>\n",
        "      <td>626.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>coadread</th>\n",
        "      <td>27110.0</td>\n",
        "      <td>1693.0</td>\n",
        "      <td>29.0</td>\n",
        "      <td>5266.0</td>\n",
        "      <td>0.937551</td>\n",
        "      <td>109.0</td>\n",
        "      <td>25417.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>39178.0</td>\n",
        "      <td>13761.0</td>\n",
        "      <td>0.0</td>\n",
        "      <td>0.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>ucec</th>\n",
        "      <td>178258.0</td>\n",
        "      <td>5156.0</td>\n",
        "      <td>118.0</td>\n",
        "      <td>25390.0</td>\n",
        "      <td>0.971076</td>\n",
        "      <td>244.0</td>\n",
        "      <td>173102.0</td>\n",
        "      <td>63.0</td>\n",
        "      <td>22761.0</td>\n",
        "      <td>237558.0</td>\n",
        "      <td>64456.0</td>\n",
        "      <td>66.0</td>\n",
        "      <td>3216.0</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 35,
       "text": [
        "          awg_variant_count  awg_variant_uniq_count  awg_variant_unvalidated  \\\n",
        "paad                 3327.0                  2218.0                      0.0   \n",
        "laml                 1396.0                   688.0                      0.0   \n",
        "prad                 5331.0                  2477.0                      5.0   \n",
        "thca                 6725.0                  2723.0                     22.0   \n",
        "luad                78158.0                 20771.0                    220.0   \n",
        "cesc                 8979.0                  1979.0                     25.0   \n",
        "gbm                 17727.0                  3067.0                      4.0   \n",
        "kirp                 6074.0                   919.0                     19.0   \n",
        "lgg                 23041.0                  3115.0                     13.0   \n",
        "stad                63600.0                  8260.0                    123.0   \n",
        "kirc                15894.0                  1995.0                      7.0   \n",
        "ov                  10140.0                  1257.0                      9.0   \n",
        "lusc                62860.0                  6626.0                     56.0   \n",
        "pancan12           512835.0                 51087.0                    520.0   \n",
        "hnsc                52688.0                  4541.0                     36.0   \n",
        "skcm               174659.0                 14467.0                     27.0   \n",
        "brca                40439.0                  3296.0                     29.0   \n",
        "blca                28165.0                  1997.0                     12.0   \n",
        "coadread            27110.0                  1693.0                     29.0   \n",
        "ucec               178258.0                  5156.0                    118.0   \n",
        "\n",
        "          awg_variant_validated  coverage  isec_samples  isec_variant_count  \\\n",
        "paad                        0.0  0.333333          26.0              1109.0   \n",
        "laml                        0.0  0.507163         127.0               708.0   \n",
        "prad                       23.0  0.535359          82.0              2854.0   \n",
        "thca                       44.0  0.595093         321.0              4002.0   \n",
        "luad                     1546.0  0.734243         192.0             57387.0   \n",
        "cesc                       68.0  0.779597          39.0              7000.0   \n",
        "gbm                       410.0  0.826987         250.0             14660.0   \n",
        "kirp                       24.0  0.848699          96.0              5155.0   \n",
        "lgg                        32.0  0.864806         170.0             19926.0   \n",
        "stad                     2362.0  0.870126         112.0             55340.0   \n",
        "kirc                       34.0  0.874481         245.0             13899.0   \n",
        "ov                        474.0  0.876036         168.0              8883.0   \n",
        "lusc                      754.0  0.894591         173.0             56234.0   \n",
        "pancan12                41079.0  0.900383        2652.0            461748.0   \n",
        "hnsc                     1643.0  0.913813         289.0             48147.0   \n",
        "skcm                      665.0  0.917170         248.0            160192.0   \n",
        "brca                     5316.0  0.918495         760.0             37143.0   \n",
        "blca                      246.0  0.929096          95.0             26168.0   \n",
        "coadread                 5266.0  0.937551         109.0             25417.0   \n",
        "ucec                    25390.0  0.971076         244.0            173102.0   \n",
        "\n",
        "          isec_variant_unvalidated  isec_variant_validated  mc3_variant_count  \\\n",
        "paad                           0.0                     0.0             1317.0   \n",
        "laml                           0.0                     0.0             5322.0   \n",
        "prad                           5.0                    98.0             3436.0   \n",
        "thca                          20.0                   769.0             8338.0   \n",
        "luad                          65.0                 12625.0            70289.0   \n",
        "cesc                          10.0                  3300.0             8191.0   \n",
        "gbm                            6.0                  1715.0            18231.0   \n",
        "kirp                           6.0                   579.0            13183.0   \n",
        "lgg                           11.0                  1103.0            23659.0   \n",
        "stad                          33.0                  6497.0            62345.0   \n",
        "kirc                           5.0                  1299.0            17310.0   \n",
        "ov                             0.0                     0.0            18547.0   \n",
        "lusc                          32.0                 10225.0            73201.0   \n",
        "pancan12                     230.0                 64912.0           636448.0   \n",
        "hnsc                          28.0                  5970.0            62316.0   \n",
        "skcm                          35.0                 28367.0           322299.0   \n",
        "brca                          10.0                  5900.0            61727.0   \n",
        "blca                          21.0                  4417.0            32769.0   \n",
        "coadread                       0.0                     0.0            39178.0   \n",
        "ucec                          63.0                 22761.0           237558.0   \n",
        "\n",
        "          mc3_variant_uniq_count  mc3_variant_unvalidated  \\\n",
        "paad                       208.0                      0.0   \n",
        "laml                      4614.0                      0.0   \n",
        "prad                       582.0                      4.0   \n",
        "thca                      4336.0                     16.0   \n",
        "luad                     12902.0                     23.0   \n",
        "cesc                      1191.0                     10.0   \n",
        "gbm                       3571.0                      7.0   \n",
        "kirp                      8028.0                      3.0   \n",
        "lgg                       3733.0                     15.0   \n",
        "stad                      7005.0                      7.0   \n",
        "kirc                      3411.0                      8.0   \n",
        "ov                        9664.0                      0.0   \n",
        "lusc                     16967.0                     11.0   \n",
        "pancan12                174700.0                    164.0   \n",
        "hnsc                     14169.0                     17.0   \n",
        "skcm                    162107.0                     31.0   \n",
        "brca                     24584.0                     29.0   \n",
        "blca                      6601.0                      3.0   \n",
        "coadread                 13761.0                      0.0   \n",
        "ucec                     64456.0                     66.0   \n",
        "\n",
        "          mc3_variant_validated  \n",
        "paad                        0.0  \n",
        "laml                        0.0  \n",
        "prad                       20.0  \n",
        "thca                       77.0  \n",
        "luad                     2133.0  \n",
        "cesc                      297.0  \n",
        "gbm                       210.0  \n",
        "kirp                       80.0  \n",
        "lgg                       104.0  \n",
        "stad                      822.0  \n",
        "kirc                      141.0  \n",
        "ov                          0.0  \n",
        "lusc                     1839.0  \n",
        "pancan12                10313.0  \n",
        "hnsc                      879.0  \n",
        "skcm                     6185.0  \n",
        "brca                     1269.0  \n",
        "blca                      626.0  \n",
        "coadread                    0.0  \n",
        "ucec                     3216.0  "
       ]
      }
     ],
     "prompt_number": 35
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "a = (df['mc3_variant_unvalidated'] / (df['mc3_variant_unvalidated']+df['mc3_variant_validated']))\n",
      "b = (df['awg_variant_unvalidated'] / (df['awg_variant_unvalidated']+df['awg_variant_validated']))\n",
      "pandas.DataFrame({\"mc3\" : a, \"awg\" : b})"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "<div style=\"max-width:1500px;overflow:auto;\">\n",
        "<table border=\"1\" class=\"dataframe\">\n",
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>awg</th>\n",
        "      <th>mc3</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>blca</th>\n",
        "      <td>0.046512</td>\n",
        "      <td>0.004769</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>brca</th>\n",
        "      <td>0.005426</td>\n",
        "      <td>0.022342</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>cesc</th>\n",
        "      <td>0.268817</td>\n",
        "      <td>0.032573</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>coadread</th>\n",
        "      <td>0.005477</td>\n",
        "      <td>NaN</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>gbm</th>\n",
        "      <td>0.009662</td>\n",
        "      <td>0.032258</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>hnsc</th>\n",
        "      <td>0.021441</td>\n",
        "      <td>0.018973</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>kirc</th>\n",
        "      <td>0.170732</td>\n",
        "      <td>0.053691</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>kirp</th>\n",
        "      <td>0.441860</td>\n",
        "      <td>0.036145</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>laml</th>\n",
        "      <td>NaN</td>\n",
        "      <td>NaN</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>lgg</th>\n",
        "      <td>0.288889</td>\n",
        "      <td>0.126050</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>luad</th>\n",
        "      <td>0.124575</td>\n",
        "      <td>0.010668</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>lusc</th>\n",
        "      <td>0.069136</td>\n",
        "      <td>0.005946</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>ov</th>\n",
        "      <td>0.018634</td>\n",
        "      <td>NaN</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>paad</th>\n",
        "      <td>NaN</td>\n",
        "      <td>NaN</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>pancan12</th>\n",
        "      <td>0.012500</td>\n",
        "      <td>0.015653</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>prad</th>\n",
        "      <td>0.178571</td>\n",
        "      <td>0.166667</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>skcm</th>\n",
        "      <td>0.039017</td>\n",
        "      <td>0.004987</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>stad</th>\n",
        "      <td>0.049497</td>\n",
        "      <td>0.008444</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>thca</th>\n",
        "      <td>0.333333</td>\n",
        "      <td>0.172043</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>ucec</th>\n",
        "      <td>0.004626</td>\n",
        "      <td>0.020110</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 42,
       "text": [
        "               awg       mc3\n",
        "blca      0.046512  0.004769\n",
        "brca      0.005426  0.022342\n",
        "cesc      0.268817  0.032573\n",
        "coadread  0.005477       NaN\n",
        "gbm       0.009662  0.032258\n",
        "hnsc      0.021441  0.018973\n",
        "kirc      0.170732  0.053691\n",
        "kirp      0.441860  0.036145\n",
        "laml           NaN       NaN\n",
        "lgg       0.288889  0.126050\n",
        "luad      0.124575  0.010668\n",
        "lusc      0.069136  0.005946\n",
        "ov        0.018634       NaN\n",
        "paad           NaN       NaN\n",
        "pancan12  0.012500  0.015653\n",
        "prad      0.178571  0.166667\n",
        "skcm      0.039017  0.004987\n",
        "stad      0.049497  0.008444\n",
        "thca      0.333333  0.172043\n",
        "ucec      0.004626  0.020110"
       ]
      }
     ],
     "prompt_number": 42
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}