Extract.sample_barcode.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from google.cloud import bigquery as bq"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Subtype"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1218, 11)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>case_barcode</th>\n",
       "      <th>aliquot_barcode</th>\n",
       "      <th>subtype</th>\n",
       "      <th>sample_barcode</th>\n",
       "      <th>ER</th>\n",
       "      <th>PR</th>\n",
       "      <th>Her2_IHC</th>\n",
       "      <th>Her2_ISH</th>\n",
       "      <th>Her2</th>\n",
       "      <th>triple_negative</th>\n",
       "      <th>subtype_sub</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-3C-AAAU</td>\n",
       "      <td>TCGA-3C-AAAU-01A-11R-A41B-07</td>\n",
       "      <td>LumA</td>\n",
       "      <td>TCGA-3C-AAAU-01A</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-3C-AALI</td>\n",
       "      <td>TCGA-3C-AALI-01A-11R-A41B-07</td>\n",
       "      <td>Her2</td>\n",
       "      <td>TCGA-3C-AALI-01A</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Her2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-3C-AALJ</td>\n",
       "      <td>TCGA-3C-AALJ-01A-31R-A41B-07</td>\n",
       "      <td>LumB</td>\n",
       "      <td>TCGA-3C-AALJ-01A</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumB</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-3C-AALK</td>\n",
       "      <td>TCGA-3C-AALK-01A-11R-A41B-07</td>\n",
       "      <td>LumA</td>\n",
       "      <td>TCGA-3C-AALK-01A</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-4H-AAAK</td>\n",
       "      <td>TCGA-4H-AAAK-01A-12R-A41B-07</td>\n",
       "      <td>LumA</td>\n",
       "      <td>TCGA-4H-AAAK-01A</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>2+</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode               aliquot_barcode subtype    sample_barcode  \\\n",
       "0  TCGA-3C-AAAU  TCGA-3C-AAAU-01A-11R-A41B-07    LumA  TCGA-3C-AAAU-01A   \n",
       "1  TCGA-3C-AALI  TCGA-3C-AALI-01A-11R-A41B-07    Her2  TCGA-3C-AALI-01A   \n",
       "2  TCGA-3C-AALJ  TCGA-3C-AALJ-01A-31R-A41B-07    LumB  TCGA-3C-AALJ-01A   \n",
       "3  TCGA-3C-AALK  TCGA-3C-AALK-01A-11R-A41B-07    LumA  TCGA-3C-AALK-01A   \n",
       "4  TCGA-4H-AAAK  TCGA-4H-AAAK-01A-12R-A41B-07    LumA  TCGA-4H-AAAK-01A   \n",
       "\n",
       "         ER        PR Her2_IHC Her2_ISH Her2 triple_negative subtype_sub  \n",
       "0  Positive  Positive      NaN      NaN  NaN             NaN        LumA  \n",
       "1  Positive  Positive      NaN      NaN  NaN             NaN        Her2  \n",
       "2  Positive  Positive      NaN      NaN  NaN             NaN        LumB  \n",
       "3  Positive  Positive      NaN      NaN  NaN             NaN        LumA  \n",
       "4  Positive  Positive       2+      NaN  NaN             NaN        LumA  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "subtypes = pd.read_table(\"./metadata/subtypes.tsv\", sep=\"\\t\")\n",
    "\n",
    "print(subtypes.shape)\n",
    "subtypes.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1218,)\n",
      "(1218, 11)\n",
      "(1097, 11)\n",
      "(1199, 11)\n"
     ]
    }
   ],
   "source": [
    "print(subtypes['sample_barcode'].drop_duplicates().shape)\n",
    "print(subtypes.drop_duplicates(subset=[\"case_barcode\", \"sample_barcode\"]).shape)\n",
    "print(subtypes.drop_duplicates(subset=[\"case_barcode\"]).shape)\n",
    "print(subtypes.drop_duplicates(subset=[\"case_barcode\", \"subtype\"]).shape)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "==>>> Only 1 aliquot barcode per sample barcode.\n",
    "\n",
    "==>>> 1 patient may have multiple samples collected. Various samples from 1 patient may be determined to be different subtypes. <br/>\n",
    "For example, case \"TCGA-BH-A0DL\" have 2 samples, 1 is Basal, another is Normal-like"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "LumA        581\n",
       "LumB        219\n",
       "Normal      143\n",
       "Basal       101\n",
       "Basal-TN     91\n",
       "Her2         82\n",
       "Name: subtype_sub, dtype: int64"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "subtypes.subtype_sub.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"'TCGA-3C-AAAU', 'TCGA-3C-AALI', 'TCGA-3C-AALJ', 'TCGA-3C-AALK', 'TCGA-4H-AAAK', 'TCGA-5L-AAT0', 'TCGA-5L-AAT1', 'TCGA-5T-A9QA', 'TCGA-A1-A0SB', 'TCGA-A1-A0SD', 'TCGA-A1-A0SE', 'TCGA-A1-A0SF', 'TCGA-A1-A0SG', 'TCGA-A1-A0SH', 'TCGA-A1-A0SI', 'TCGA-A1-A0SJ', 'TCGA-A1-A0SK', 'TCGA-A1-A0SM', 'TCGA-A1-A0SN', 'TCGA-A1-A0SO', 'TCGA-A1-A0SP', 'TCGA-A1-A0SQ', 'TCGA-A2-A04N', 'TCGA-A2-A04P', 'TCGA-A2-A04Q', 'TCGA-A2-A04R', 'TCGA-A2-A04T', 'TCGA-A2-A04U', 'TCGA-A2-A04V', 'TCGA-A2-A04W', 'TCGA-A2-A04X', 'TCGA-A2-A04Y', 'TCGA-A2-A0CK', 'TCGA-A2-A0CL', 'TCGA-A2-A0CM', 'TCGA-A2-A0CO', 'TCGA-A2-A0CP', 'TCGA-A2-A0CQ', 'TCGA-A2-A0CR', 'TCGA-A2-A0CS', 'TCGA-A2-A0CT', 'TCGA-A2-A0CU', 'TCGA-A2-A0CV', 'TCGA-A2-A0CW', 'TCGA-A2-A0CX', 'TCGA-A2-A0CY', 'TCGA-A2-A0CZ', 'TCGA-A2-A0D0', 'TCGA-A2-A0D1', 'TCGA-A2-A0D2', 'TCGA-A2-A0D3', 'TCGA-A2-A0D4', 'TCGA-A2-A0EM', 'TCGA-A2-A0EN', 'TCGA-A2-A0EO', 'TCGA-A2-A0EP', 'TCGA-A2-A0EQ', 'TCGA-A2-A0ER', 'TCGA-A2-A0ES', 'TCGA-A2-A0ET', 'TCGA-A2-A0EU', 'TCGA-A2-A0EV', 'TCGA-A2-A0EW', 'TCGA-A2-A0EX', 'TCGA-A2-A0EY', 'TCGA-A2-A0ST', 'TCGA-A2-A0SU', 'TCGA-A2-A0SV', 'TCGA-A2-A0SW', 'TCGA-A2-A0SX', 'TCGA-A2-A0SY', 'TCGA-A2-A0T0', 'TCGA-A2-A0T1', 'TCGA-A2-A0T2', 'TCGA-A2-A0T3', 'TCGA-A2-A0T4', 'TCGA-A2-A0T5', 'TCGA-A2-A0T6', 'TCGA-A2-A0T7', 'TCGA-A2-A0YC', 'TCGA-A2-A0YD', 'TCGA-A2-A0YE', 'TCGA-A2-A0YF', 'TCGA-A2-A0YG', 'TCGA-A2-A0YH', 'TCGA-A2-A0YI', 'TCGA-A2-A0YJ', 'TCGA-A2-A0YK', 'TCGA-A2-A0YL', 'TCGA-A2-A0YM', 'TCGA-A2-A0YT', 'TCGA-A2-A1FV', 'TCGA-A2-A1FW', 'TCGA-A2-A1FX', 'TCGA-A2-A1FZ', 'TCGA-A2-A1G0', 'TCGA-A2-A1G1', 'TCGA-A2-A1G4', 'TCGA-A2-A1G6', 'TCGA-A2-A259', 'TCGA-A2-A25A', 'TCGA-A2-A25B', 'TCGA-A2-A25C', 'TCGA-A2-A25D', 'TCGA-A2-A25E', 'TCGA-A2-A25F', 'TCGA-A2-A3KC', 'TCGA-A2-A3KD', 'TCGA-A2-A3XS', 'TCGA-A2-A3XT', 'TCGA-A2-A3XU', 'TCGA-A2-A3XV', 'TCGA-A2-A3XW', 'TCGA-A2-A3XX', 'TCGA-A2-A3XY', 'TCGA-A2-A3XZ', 'TCGA-A2-A3Y0', 'TCGA-A2-A4RW', 'TCGA-A2-A4RX', 'TCGA-A2-A4RY', 'TCGA-A2-A4S0', 'TCGA-A2-A4S1', 'TCGA-A2-A4S2', 'TCGA-A2-A4S3', 'TCGA-A7-A0CD', 'TCGA-A7-A0CE', 'TCGA-A7-A0CE', 'TCGA-A7-A0CG', 'TCGA-A7-A0CH', 'TCGA-A7-A0CH', 'TCGA-A7-A0CJ', 'TCGA-A7-A0D9', 'TCGA-A7-A0D9', 'TCGA-A7-A0DA', 'TCGA-A7-A0DB', 'TCGA-A7-A0DB', 'TCGA-A7-A0DC', 'TCGA-A7-A0DC', 'TCGA-A7-A13D', 'TCGA-A7-A13E', 'TCGA-A7-A13E', 'TCGA-A7-A13F', 'TCGA-A7-A13F', 'TCGA-A7-A13G', 'TCGA-A7-A13G', 'TCGA-A7-A13H', 'TCGA-A7-A26E', 'TCGA-A7-A26F', 'TCGA-A7-A26G', 'TCGA-A7-A26H', 'TCGA-A7-A26I', 'TCGA-A7-A26J', 'TCGA-A7-A2KD', 'TCGA-A7-A3IY', 'TCGA-A7-A3IZ', 'TCGA-A7-A3J0', 'TCGA-A7-A3J1', 'TCGA-A7-A3RF', 'TCGA-A7-A425', 'TCGA-A7-A426', 'TCGA-A7-A4SA', 'TCGA-A7-A4SB', 'TCGA-A7-A4SC', 'TCGA-A7-A4SD', 'TCGA-A7-A4SE', 'TCGA-A7-A4SF', 'TCGA-A7-A56D', 'TCGA-A7-A5ZV', 'TCGA-A7-A5ZW', 'TCGA-A7-A5ZX', 'TCGA-A7-A6VV', 'TCGA-A7-A6VW', 'TCGA-A7-A6VX', 'TCGA-A7-A6VY', 'TCGA-A8-A06N', 'TCGA-A8-A06O', 'TCGA-A8-A06P', 'TCGA-A8-A06Q', 'TCGA-A8-A06R', 'TCGA-A8-A06T', 'TCGA-A8-A06U', 'TCGA-A8-A06X', 'TCGA-A8-A06Y', 'TCGA-A8-A06Z', 'TCGA-A8-A075', 'TCGA-A8-A076', 'TCGA-A8-A079', 'TCGA-A8-A07B', 'TCGA-A8-A07C', 'TCGA-A8-A07E', 'TCGA-A8-A07F', 'TCGA-A8-A07G', 'TCGA-A8-A07I', 'TCGA-A8-A07J', 'TCGA-A8-A07L', 'TCGA-A8-A07O', 'TCGA-A8-A07P', 'TCGA-A8-A07R', 'TCGA-A8-A07S', 'TCGA-A8-A07U', 'TCGA-A8-A07W', 'TCGA-A8-A07Z', 'TCGA-A8-A081', 'TCGA-A8-A082', 'TCGA-A8-A083', 'TCGA-A8-A084', 'TCGA-A8-A085', 'TCGA-A8-A086', 'TCGA-A8-A08A', 'TCGA-A8-A08B', 'TCGA-A8-A08C', 'TCGA-A8-A08F', 'TCGA-A8-A08G', 'TCGA-A8-A08H', 'TCGA-A8-A08I', 'TCGA-A8-A08J', 'TCGA-A8-A08L', 'TCGA-A8-A08O', 'TCGA-A8-A08P', 'TCGA-A8-A08R', 'TCGA-A8-A08S', 'TCGA-A8-A08T', 'TCGA-A8-A08X', 'TCGA-A8-A08Z', 'TCGA-A8-A090', 'TCGA-A8-A091', 'TCGA-A8-A092', 'TCGA-A8-A093', 'TCGA-A8-A094', 'TCGA-A8-A095', 'TCGA-A8-A096', 'TCGA-A8-A097', 'TCGA-A8-A099', 'TCGA-A8-A09A', 'TCGA-A8-A09B', 'TCGA-A8-A09C', 'TCGA-A8-A09D', 'TCGA-A8-A09E', 'TCGA-A8-A09G', 'TCGA-A8-A09I', 'TCGA-A8-A09K', 'TCGA-A8-A09M', 'TCGA-A8-A09N', 'TCGA-A8-A09Q', 'TCGA-A8-A09R', 'TCGA-A8-A09T', 'TCGA-A8-A09V', 'TCGA-A8-A09W', 'TCGA-A8-A09X', 'TCGA-A8-A09Z', 'TCGA-A8-A0A1', 'TCGA-A8-A0A2', 'TCGA-A8-A0A4', 'TCGA-A8-A0A6', 'TCGA-A8-A0A7', 'TCGA-A8-A0A9', 'TCGA-A8-A0AB', 'TCGA-A8-A0AD', 'TCGA-AC-A23C', 'TCGA-AC-A23E', 'TCGA-AC-A23G', 'TCGA-AC-A23H', 'TCGA-AC-A23H', 'TCGA-AC-A2B8', 'TCGA-AC-A2BK', 'TCGA-AC-A2BM', 'TCGA-AC-A2FB', 'TCGA-AC-A2FB', 'TCGA-AC-A2FE', 'TCGA-AC-A2FF', 'TCGA-AC-A2FF', 'TCGA-AC-A2FG', 'TCGA-AC-A2FK', 'TCGA-AC-A2FM', 'TCGA-AC-A2FM', 'TCGA-AC-A2FO', 'TCGA-AC-A2QH', 'TCGA-AC-A2QI', 'TCGA-AC-A2QJ', 'TCGA-AC-A3BB', 'TCGA-AC-A3EH', 'TCGA-AC-A3HN', 'TCGA-AC-A3OD', 'TCGA-AC-A3QP', 'TCGA-AC-A3QQ', 'TCGA-AC-A3TM', 'TCGA-AC-A3TN', 'TCGA-AC-A3W5', 'TCGA-AC-A3W6', 'TCGA-AC-A3W7', 'TCGA-AC-A3YI', 'TCGA-AC-A3YJ', 'TCGA-AC-A4ZE', 'TCGA-AC-A5EH', 'TCGA-AC-A5XS', 'TCGA-AC-A5XU', 'TCGA-AC-A62V', 'TCGA-AC-A62X', 'TCGA-AC-A62Y', 'TCGA-AC-A6IV', 'TCGA-AC-A6IW', 'TCGA-AC-A6IX', 'TCGA-AC-A6IX', 'TCGA-AC-A6NO', 'TCGA-AC-A7VB', 'TCGA-AC-A7VC', 'TCGA-AC-A8OP', 'TCGA-AC-A8OQ', 'TCGA-AC-A8OR', 'TCGA-AC-A8OS', 'TCGA-AN-A03X', 'TCGA-AN-A03Y', 'TCGA-AN-A041', 'TCGA-AN-A046', 'TCGA-AN-A049', 'TCGA-AN-A04A', 'TCGA-AN-A04C', 'TCGA-AN-A04D', 'TCGA-AN-A0AJ', 'TCGA-AN-A0AK', 'TCGA-AN-A0AL', 'TCGA-AN-A0AM', 'TCGA-AN-A0AR', 'TCGA-AN-A0AS', 'TCGA-AN-A0AT', 'TCGA-AN-A0FD', 'TCGA-AN-A0FF', 'TCGA-AN-A0FJ', 'TCGA-AN-A0FK', 'TCGA-AN-A0FL', 'TCGA-AN-A0FN', 'TCGA-AN-A0FS', 'TCGA-AN-A0FT', 'TCGA-AN-A0FV', 'TCGA-AN-A0FW', 'TCGA-AN-A0FX', 'TCGA-AN-A0FY', 'TCGA-AN-A0FZ', 'TCGA-AN-A0G0', 'TCGA-AN-A0XL', 'TCGA-AN-A0XN', 'TCGA-AN-A0XO', 'TCGA-AN-A0XP', 'TCGA-AN-A0XR', 'TCGA-AN-A0XS', 'TCGA-AN-A0XT', 'TCGA-AN-A0XU', 'TCGA-AN-A0XV', 'TCGA-AN-A0XW', 'TCGA-AO-A03L', 'TCGA-AO-A03M', 'TCGA-AO-A03N', 'TCGA-AO-A03O', 'TCGA-AO-A03P', 'TCGA-AO-A03R', 'TCGA-AO-A03T', 'TCGA-AO-A03U', 'TCGA-AO-A03V', 'TCGA-AO-A0J2', 'TCGA-AO-A0J3', 'TCGA-AO-A0J4', 'TCGA-AO-A0J5', 'TCGA-AO-A0J6', 'TCGA-AO-A0J7', 'TCGA-AO-A0J8', 'TCGA-AO-A0J9', 'TCGA-AO-A0JA', 'TCGA-AO-A0JB', 'TCGA-AO-A0JC', 'TCGA-AO-A0JD', 'TCGA-AO-A0JE', 'TCGA-AO-A0JF', 'TCGA-AO-A0JG', 'TCGA-AO-A0JI', 'TCGA-AO-A0JJ', 'TCGA-AO-A0JL', 'TCGA-AO-A0JM', 'TCGA-AO-A124', 'TCGA-AO-A125', 'TCGA-AO-A126', 'TCGA-AO-A128', 'TCGA-AO-A129', 'TCGA-AO-A12A', 'TCGA-AO-A12B', 'TCGA-AO-A12C', 'TCGA-AO-A12D', 'TCGA-AO-A12E', 'TCGA-AO-A12F', 'TCGA-AO-A12G', 'TCGA-AO-A12H', 'TCGA-AO-A1KO', 'TCGA-AO-A1KP', 'TCGA-AO-A1KQ', 'TCGA-AO-A1KR', 'TCGA-AO-A1KS', 'TCGA-AO-A1KT', 'TCGA-AQ-A04H', 'TCGA-AQ-A04J', 'TCGA-AQ-A04L', 'TCGA-AQ-A0Y5', 'TCGA-AQ-A1H2', 'TCGA-AQ-A1H3', 'TCGA-AQ-A54N', 'TCGA-AQ-A54O', 'TCGA-AQ-A7U7', 'TCGA-AR-A0TP', 'TCGA-AR-A0TQ', 'TCGA-AR-A0TR', 'TCGA-AR-A0TS', 'TCGA-AR-A0TT', 'TCGA-AR-A0TU', 'TCGA-AR-A0TV', 'TCGA-AR-A0TW', 'TCGA-AR-A0TX', 'TCGA-AR-A0TY', 'TCGA-AR-A0TZ', 'TCGA-AR-A0U0', 'TCGA-AR-A0U1', 'TCGA-AR-A0U2', 'TCGA-AR-A0U3', 'TCGA-AR-A0U4', 'TCGA-AR-A1AH', 'TCGA-AR-A1AI', 'TCGA-AR-A1AJ', 'TCGA-AR-A1AK', 'TCGA-AR-A1AL', 'TCGA-AR-A1AM', 'TCGA-AR-A1AN', 'TCGA-AR-A1AO', 'TCGA-AR-A1AP', 'TCGA-AR-A1AQ', 'TCGA-AR-A1AR', 'TCGA-AR-A1AS', 'TCGA-AR-A1AT', 'TCGA-AR-A1AU', 'TCGA-AR-A1AV', 'TCGA-AR-A1AW', 'TCGA-AR-A1AX', 'TCGA-AR-A1AY', 'TCGA-AR-A24H', 'TCGA-AR-A24K', 'TCGA-AR-A24L', 'TCGA-AR-A24M', 'TCGA-AR-A24N', 'TCGA-AR-A24O', 'TCGA-AR-A24P', 'TCGA-AR-A24Q', 'TCGA-AR-A24R', 'TCGA-AR-A24S', 'TCGA-AR-A24T', 'TCGA-AR-A24U', 'TCGA-AR-A24V', 'TCGA-AR-A24W', 'TCGA-AR-A24X', 'TCGA-AR-A24Z', 'TCGA-AR-A250', 'TCGA-AR-A251', 'TCGA-AR-A252', 'TCGA-AR-A254', 'TCGA-AR-A255', 'TCGA-AR-A256', 'TCGA-AR-A2LE', 'TCGA-AR-A2LH', 'TCGA-AR-A2LJ', 'TCGA-AR-A2LK', 'TCGA-AR-A2LL', 'TCGA-AR-A2LM', 'TCGA-AR-A2LN', 'TCGA-AR-A2LO', 'TCGA-AR-A2LQ', 'TCGA-AR-A2LR', 'TCGA-AR-A5QM', 'TCGA-AR-A5QN', 'TCGA-AR-A5QP', 'TCGA-AR-A5QQ', 'TCGA-B6-A0I1', 'TCGA-B6-A0I2', 'TCGA-B6-A0I5', 'TCGA-B6-A0I6', 'TCGA-B6-A0I8', 'TCGA-B6-A0I9', 'TCGA-B6-A0IA', 'TCGA-B6-A0IB', 'TCGA-B6-A0IC', 'TCGA-B6-A0IE', 'TCGA-B6-A0IG', 'TCGA-B6-A0IH', 'TCGA-B6-A0IJ', 'TCGA-B6-A0IK', 'TCGA-B6-A0IM', 'TCGA-B6-A0IN', 'TCGA-B6-A0IO', 'TCGA-B6-A0IP', 'TCGA-B6-A0IQ', 'TCGA-B6-A0RE', 'TCGA-B6-A0RG', 'TCGA-B6-A0RH', 'TCGA-B6-A0RI', 'TCGA-B6-A0RL', 'TCGA-B6-A0RM', 'TCGA-B6-A0RN', 'TCGA-B6-A0RO', 'TCGA-B6-A0RP', 'TCGA-B6-A0RQ', 'TCGA-B6-A0RS', 'TCGA-B6-A0RT', 'TCGA-B6-A0RU', 'TCGA-B6-A0RV', 'TCGA-B6-A0WS', 'TCGA-B6-A0WT', 'TCGA-B6-A0WV', 'TCGA-B6-A0WW', 'TCGA-B6-A0WX', 'TCGA-B6-A0WY', 'TCGA-B6-A0WZ', 'TCGA-B6-A0X0', 'TCGA-B6-A0X1', 'TCGA-B6-A0X4', 'TCGA-B6-A0X5', 'TCGA-B6-A0X7', 'TCGA-B6-A1KC', 'TCGA-B6-A1KF', 'TCGA-B6-A1KI', 'TCGA-B6-A1KN', 'TCGA-B6-A2IU', 'TCGA-B6-A3ZX', 'TCGA-B6-A400', 'TCGA-B6-A401', 'TCGA-B6-A402', 'TCGA-B6-A408', 'TCGA-B6-A409', 'TCGA-B6-A40B', 'TCGA-B6-A40C', 'TCGA-BH-A0AU', 'TCGA-BH-A0AU', 'TCGA-BH-A0AV', 'TCGA-BH-A0AW', 'TCGA-BH-A0AY', 'TCGA-BH-A0AY', 'TCGA-BH-A0AZ', 'TCGA-BH-A0AZ', 'TCGA-BH-A0B0', 'TCGA-BH-A0B1', 'TCGA-BH-A0B2', 'TCGA-BH-A0B2', 'TCGA-BH-A0B3', 'TCGA-BH-A0B3', 'TCGA-BH-A0B4', 'TCGA-BH-A0B5', 'TCGA-BH-A0B5', 'TCGA-BH-A0B6', 'TCGA-BH-A0B7', 'TCGA-BH-A0B7', 'TCGA-BH-A0B8', 'TCGA-BH-A0B8', 'TCGA-BH-A0B9', 'TCGA-BH-A0BA', 'TCGA-BH-A0BA', 'TCGA-BH-A0BC', 'TCGA-BH-A0BC', 'TCGA-BH-A0BD', 'TCGA-BH-A0BF', 'TCGA-BH-A0BG', 'TCGA-BH-A0BJ', 'TCGA-BH-A0BJ', 'TCGA-BH-A0BL', 'TCGA-BH-A0BM', 'TCGA-BH-A0BM', 'TCGA-BH-A0BO', 'TCGA-BH-A0BP', 'TCGA-BH-A0BQ', 'TCGA-BH-A0BQ', 'TCGA-BH-A0BR', 'TCGA-BH-A0BS', 'TCGA-BH-A0BS', 'TCGA-BH-A0BT', 'TCGA-BH-A0BT', 'TCGA-BH-A0BV', 'TCGA-BH-A0BV', 'TCGA-BH-A0BW', 'TCGA-BH-A0BW', 'TCGA-BH-A0BZ', 'TCGA-BH-A0BZ', 'TCGA-BH-A0C0', 'TCGA-BH-A0C0', 'TCGA-BH-A0C1', 'TCGA-BH-A0C3', 'TCGA-BH-A0C3', 'TCGA-BH-A0C7', 'TCGA-BH-A0DD', 'TCGA-BH-A0DD', 'TCGA-BH-A0DE', 'TCGA-BH-A0DG', 'TCGA-BH-A0DG', 'TCGA-BH-A0DH', 'TCGA-BH-A0DH', 'TCGA-BH-A0DI', 'TCGA-BH-A0DK', 'TCGA-BH-A0DK', 'TCGA-BH-A0DL', 'TCGA-BH-A0DL', 'TCGA-BH-A0DO', 'TCGA-BH-A0DO', 'TCGA-BH-A0DP', 'TCGA-BH-A0DP', 'TCGA-BH-A0DQ', 'TCGA-BH-A0DQ', 'TCGA-BH-A0DS', 'TCGA-BH-A0DT', 'TCGA-BH-A0DT', 'TCGA-BH-A0DV', 'TCGA-BH-A0DV', 'TCGA-BH-A0DX', 'TCGA-BH-A0DZ', 'TCGA-BH-A0DZ', 'TCGA-BH-A0E0', 'TCGA-BH-A0E0', 'TCGA-BH-A0E1', 'TCGA-BH-A0E1', 'TCGA-BH-A0E2', 'TCGA-BH-A0E6', 'TCGA-BH-A0E7', 'TCGA-BH-A0E9', 'TCGA-BH-A0EA', 'TCGA-BH-A0EB', 'TCGA-BH-A0EE', 'TCGA-BH-A0EI', 'TCGA-BH-A0GY', 'TCGA-BH-A0GZ', 'TCGA-BH-A0H0', 'TCGA-BH-A0H3', 'TCGA-BH-A0H5', 'TCGA-BH-A0H5', 'TCGA-BH-A0H6', 'TCGA-BH-A0H7', 'TCGA-BH-A0H7', 'TCGA-BH-A0H9', 'TCGA-BH-A0H9', 'TCGA-BH-A0HA', 'TCGA-BH-A0HA', 'TCGA-BH-A0HB', 'TCGA-BH-A0HF', 'TCGA-BH-A0HI', 'TCGA-BH-A0HK', 'TCGA-BH-A0HK', 'TCGA-BH-A0HL', 'TCGA-BH-A0HN', 'TCGA-BH-A0HO', 'TCGA-BH-A0HP', 'TCGA-BH-A0HQ', 'TCGA-BH-A0HU', 'TCGA-BH-A0HW', 'TCGA-BH-A0HX', 'TCGA-BH-A0HY', 'TCGA-BH-A0RX', 'TCGA-BH-A0W3', 'TCGA-BH-A0W4', 'TCGA-BH-A0W5', 'TCGA-BH-A0W7', 'TCGA-BH-A0WA', 'TCGA-BH-A18F', 'TCGA-BH-A18G', 'TCGA-BH-A18H', 'TCGA-BH-A18I', 'TCGA-BH-A18J', 'TCGA-BH-A18J', 'TCGA-BH-A18K', 'TCGA-BH-A18K', 'TCGA-BH-A18L', 'TCGA-BH-A18L', 'TCGA-BH-A18M', 'TCGA-BH-A18M', 'TCGA-BH-A18N', 'TCGA-BH-A18N', 'TCGA-BH-A18P', 'TCGA-BH-A18P', 'TCGA-BH-A18Q', 'TCGA-BH-A18Q', 'TCGA-BH-A18R', 'TCGA-BH-A18R', 'TCGA-BH-A18S', 'TCGA-BH-A18S', 'TCGA-BH-A18T', 'TCGA-BH-A18U', 'TCGA-BH-A18U', 'TCGA-BH-A18V', 'TCGA-BH-A18V', 'TCGA-BH-A18V', 'TCGA-BH-A1EN', 'TCGA-BH-A1EN', 'TCGA-BH-A1EO', 'TCGA-BH-A1EO', 'TCGA-BH-A1ES', 'TCGA-BH-A1ES', 'TCGA-BH-A1ET', 'TCGA-BH-A1ET', 'TCGA-BH-A1EU', 'TCGA-BH-A1EU', 'TCGA-BH-A1EV', 'TCGA-BH-A1EV', 'TCGA-BH-A1EW', 'TCGA-BH-A1EW', 'TCGA-BH-A1EX', 'TCGA-BH-A1EY', 'TCGA-BH-A1F0', 'TCGA-BH-A1F0', 'TCGA-BH-A1F2', 'TCGA-BH-A1F2', 'TCGA-BH-A1F5', 'TCGA-BH-A1F6', 'TCGA-BH-A1F6', 'TCGA-BH-A1F8', 'TCGA-BH-A1F8', 'TCGA-BH-A1FB', 'TCGA-BH-A1FB', 'TCGA-BH-A1FC', 'TCGA-BH-A1FC', 'TCGA-BH-A1FD', 'TCGA-BH-A1FD', 'TCGA-BH-A1FE', 'TCGA-BH-A1FE', 'TCGA-BH-A1FE', 'TCGA-BH-A1FG', 'TCGA-BH-A1FG', 'TCGA-BH-A1FH', 'TCGA-BH-A1FH', 'TCGA-BH-A1FJ', 'TCGA-BH-A1FJ', 'TCGA-BH-A1FL', 'TCGA-BH-A1FM', 'TCGA-BH-A1FM', 'TCGA-BH-A1FN', 'TCGA-BH-A1FN', 'TCGA-BH-A1FR', 'TCGA-BH-A1FR', 'TCGA-BH-A1FU', 'TCGA-BH-A1FU', 'TCGA-BH-A201', 'TCGA-BH-A202', 'TCGA-BH-A203', 'TCGA-BH-A203', 'TCGA-BH-A204', 'TCGA-BH-A204', 'TCGA-BH-A208', 'TCGA-BH-A208', 'TCGA-BH-A209', 'TCGA-BH-A209', 'TCGA-BH-A28O', 'TCGA-BH-A28Q', 'TCGA-BH-A2L8', 'TCGA-BH-A42T', 'TCGA-BH-A42U', 'TCGA-BH-A42V', 'TCGA-BH-A5IZ', 'TCGA-BH-A5J0', 'TCGA-BH-A6R8', 'TCGA-BH-A6R9', 'TCGA-BH-A8FY', 'TCGA-BH-A8FZ', 'TCGA-BH-A8G0', 'TCGA-BH-AB28', 'TCGA-C8-A12K', 'TCGA-C8-A12L', 'TCGA-C8-A12M', 'TCGA-C8-A12N', 'TCGA-C8-A12O', 'TCGA-C8-A12P', 'TCGA-C8-A12Q', 'TCGA-C8-A12T', 'TCGA-C8-A12U', 'TCGA-C8-A12V', 'TCGA-C8-A12W', 'TCGA-C8-A12X', 'TCGA-C8-A12Y', 'TCGA-C8-A12Z', 'TCGA-C8-A130', 'TCGA-C8-A131', 'TCGA-C8-A132', 'TCGA-C8-A133', 'TCGA-C8-A134', 'TCGA-C8-A135', 'TCGA-C8-A137', 'TCGA-C8-A138', 'TCGA-C8-A1HE', 'TCGA-C8-A1HF', 'TCGA-C8-A1HG', 'TCGA-C8-A1HI', 'TCGA-C8-A1HJ', 'TCGA-C8-A1HK', 'TCGA-C8-A1HL', 'TCGA-C8-A1HM', 'TCGA-C8-A1HN', 'TCGA-C8-A1HO', 'TCGA-C8-A26V', 'TCGA-C8-A26W', 'TCGA-C8-A26X', 'TCGA-C8-A26Y', 'TCGA-C8-A26Z', 'TCGA-C8-A273', 'TCGA-C8-A274', 'TCGA-C8-A275', 'TCGA-C8-A278', 'TCGA-C8-A27A', 'TCGA-C8-A27B', 'TCGA-C8-A3M7', 'TCGA-C8-A3M8', 'TCGA-C8-A8HP', 'TCGA-C8-A8HQ', 'TCGA-C8-A8HR', 'TCGA-D8-A13Y', 'TCGA-D8-A13Z', 'TCGA-D8-A140', 'TCGA-D8-A141', 'TCGA-D8-A142', 'TCGA-D8-A143', 'TCGA-D8-A145', 'TCGA-D8-A146', 'TCGA-D8-A147', 'TCGA-D8-A1J8', 'TCGA-D8-A1J9', 'TCGA-D8-A1JA', 'TCGA-D8-A1JB', 'TCGA-D8-A1JC', 'TCGA-D8-A1JD', 'TCGA-D8-A1JE', 'TCGA-D8-A1JF', 'TCGA-D8-A1JG', 'TCGA-D8-A1JH', 'TCGA-D8-A1JI', 'TCGA-D8-A1JJ', 'TCGA-D8-A1JK', 'TCGA-D8-A1JL', 'TCGA-D8-A1JM', 'TCGA-D8-A1JN', 'TCGA-D8-A1JP', 'TCGA-D8-A1JS', 'TCGA-D8-A1JT', 'TCGA-D8-A1JU', 'TCGA-D8-A1X5', 'TCGA-D8-A1X6', 'TCGA-D8-A1X7', 'TCGA-D8-A1X8', 'TCGA-D8-A1X9', 'TCGA-D8-A1XA', 'TCGA-D8-A1XB', 'TCGA-D8-A1XC', 'TCGA-D8-A1XD', 'TCGA-D8-A1XF', 'TCGA-D8-A1XG', 'TCGA-D8-A1XJ', 'TCGA-D8-A1XK', 'TCGA-D8-A1XL', 'TCGA-D8-A1XM', 'TCGA-D8-A1XO', 'TCGA-D8-A1XQ', 'TCGA-D8-A1XR', 'TCGA-D8-A1XS', 'TCGA-D8-A1XT', 'TCGA-D8-A1XU', 'TCGA-D8-A1XV', 'TCGA-D8-A1XW', 'TCGA-D8-A1XY', 'TCGA-D8-A1XZ', 'TCGA-D8-A1Y0', 'TCGA-D8-A1Y1', 'TCGA-D8-A1Y2', 'TCGA-D8-A1Y3', 'TCGA-D8-A27E', 'TCGA-D8-A27F', 'TCGA-D8-A27G', 'TCGA-D8-A27H', 'TCGA-D8-A27I', 'TCGA-D8-A27K', 'TCGA-D8-A27L', 'TCGA-D8-A27M', 'TCGA-D8-A27N', 'TCGA-D8-A27P', 'TCGA-D8-A27R', 'TCGA-D8-A27T', 'TCGA-D8-A27V', 'TCGA-D8-A27W', 'TCGA-D8-A3Z5', 'TCGA-D8-A3Z6', 'TCGA-D8-A4Z1', 'TCGA-D8-A73U', 'TCGA-D8-A73W', 'TCGA-D8-A73X', 'TCGA-E2-A105', 'TCGA-E2-A106', 'TCGA-E2-A107', 'TCGA-E2-A108', 'TCGA-E2-A109', 'TCGA-E2-A10A', 'TCGA-E2-A10B', 'TCGA-E2-A10C', 'TCGA-E2-A10E', 'TCGA-E2-A10F', 'TCGA-E2-A14N', 'TCGA-E2-A14O', 'TCGA-E2-A14P', 'TCGA-E2-A14Q', 'TCGA-E2-A14R', 'TCGA-E2-A14S', 'TCGA-E2-A14T', 'TCGA-E2-A14U', 'TCGA-E2-A14V', 'TCGA-E2-A14W', 'TCGA-E2-A14X', 'TCGA-E2-A14Y', 'TCGA-E2-A14Z', 'TCGA-E2-A150', 'TCGA-E2-A152', 'TCGA-E2-A153', 'TCGA-E2-A153', 'TCGA-E2-A154', 'TCGA-E2-A155', 'TCGA-E2-A156', 'TCGA-E2-A158', 'TCGA-E2-A158', 'TCGA-E2-A159', 'TCGA-E2-A15A', 'TCGA-E2-A15A', 'TCGA-E2-A15C', 'TCGA-E2-A15D', 'TCGA-E2-A15E', 'TCGA-E2-A15E', 'TCGA-E2-A15F', 'TCGA-E2-A15G', 'TCGA-E2-A15H', 'TCGA-E2-A15I', 'TCGA-E2-A15I', 'TCGA-E2-A15J', 'TCGA-E2-A15K', 'TCGA-E2-A15K', 'TCGA-E2-A15K', 'TCGA-E2-A15L', 'TCGA-E2-A15M', 'TCGA-E2-A15M', 'TCGA-E2-A15O', 'TCGA-E2-A15P', 'TCGA-E2-A15R', 'TCGA-E2-A15S', 'TCGA-E2-A15T', 'TCGA-E2-A1AZ', 'TCGA-E2-A1B0', 'TCGA-E2-A1B1', 'TCGA-E2-A1B4', 'TCGA-E2-A1B5', 'TCGA-E2-A1B6', 'TCGA-E2-A1BC', 'TCGA-E2-A1BC', 'TCGA-E2-A1BD', 'TCGA-E2-A1IE', 'TCGA-E2-A1IF', 'TCGA-E2-A1IG', 'TCGA-E2-A1IG', 'TCGA-E2-A1IH', 'TCGA-E2-A1II', 'TCGA-E2-A1IJ', 'TCGA-E2-A1IK', 'TCGA-E2-A1IL', 'TCGA-E2-A1IN', 'TCGA-E2-A1IO', 'TCGA-E2-A1IP', 'TCGA-E2-A1IU', 'TCGA-E2-A1L6', 'TCGA-E2-A1L7', 'TCGA-E2-A1L7', 'TCGA-E2-A1L8', 'TCGA-E2-A1L9', 'TCGA-E2-A1LA', 'TCGA-E2-A1LB', 'TCGA-E2-A1LB', 'TCGA-E2-A1LE', 'TCGA-E2-A1LG', 'TCGA-E2-A1LH', 'TCGA-E2-A1LH', 'TCGA-E2-A1LI', 'TCGA-E2-A1LK', 'TCGA-E2-A1LL', 'TCGA-E2-A1LS', 'TCGA-E2-A1LS', 'TCGA-E2-A2P5', 'TCGA-E2-A2P6', 'TCGA-E2-A3DX', 'TCGA-E2-A56Z', 'TCGA-E2-A570', 'TCGA-E2-A572', 'TCGA-E2-A573', 'TCGA-E2-A574', 'TCGA-E2-A576', 'TCGA-E2-A9RU', 'TCGA-E9-A1N3', 'TCGA-E9-A1N4', 'TCGA-E9-A1N4', 'TCGA-E9-A1N5', 'TCGA-E9-A1N5', 'TCGA-E9-A1N6', 'TCGA-E9-A1N6', 'TCGA-E9-A1N8', 'TCGA-E9-A1N9', 'TCGA-E9-A1N9', 'TCGA-E9-A1NA', 'TCGA-E9-A1NA', 'TCGA-E9-A1NC', 'TCGA-E9-A1ND', 'TCGA-E9-A1ND', 'TCGA-E9-A1NE', 'TCGA-E9-A1NF', 'TCGA-E9-A1NF', 'TCGA-E9-A1NG', 'TCGA-E9-A1NG', 'TCGA-E9-A1NH', 'TCGA-E9-A1NI', 'TCGA-E9-A1QZ', 'TCGA-E9-A1R0', 'TCGA-E9-A1R2', 'TCGA-E9-A1R3', 'TCGA-E9-A1R4', 'TCGA-E9-A1R5', 'TCGA-E9-A1R6', 'TCGA-E9-A1R7', 'TCGA-E9-A1R7', 'TCGA-E9-A1RA', 'TCGA-E9-A1RB', 'TCGA-E9-A1RB', 'TCGA-E9-A1RC', 'TCGA-E9-A1RC', 'TCGA-E9-A1RD', 'TCGA-E9-A1RD', 'TCGA-E9-A1RE', 'TCGA-E9-A1RF', 'TCGA-E9-A1RF', 'TCGA-E9-A1RG', 'TCGA-E9-A1RH', 'TCGA-E9-A1RH', 'TCGA-E9-A1RI', 'TCGA-E9-A1RI', 'TCGA-E9-A226', 'TCGA-E9-A227', 'TCGA-E9-A228', 'TCGA-E9-A229', 'TCGA-E9-A22A', 'TCGA-E9-A22B', 'TCGA-E9-A22D', 'TCGA-E9-A22E', 'TCGA-E9-A22G', 'TCGA-E9-A22H', 'TCGA-E9-A243', 'TCGA-E9-A244', 'TCGA-E9-A245', 'TCGA-E9-A247', 'TCGA-E9-A248', 'TCGA-E9-A249', 'TCGA-E9-A24A', 'TCGA-E9-A295', 'TCGA-E9-A2JS', 'TCGA-E9-A2JT', 'TCGA-E9-A3HO', 'TCGA-E9-A3Q9', 'TCGA-E9-A3QA', 'TCGA-E9-A3X8', 'TCGA-E9-A54X', 'TCGA-E9-A54Y', 'TCGA-E9-A5FK', 'TCGA-E9-A5FL', 'TCGA-E9-A5UO', 'TCGA-E9-A5UP', 'TCGA-E9-A6HE', 'TCGA-EW-A1IW', 'TCGA-EW-A1IX', 'TCGA-EW-A1IY', 'TCGA-EW-A1IZ', 'TCGA-EW-A1J1', 'TCGA-EW-A1J2', 'TCGA-EW-A1J3', 'TCGA-EW-A1J5', 'TCGA-EW-A1J6', 'TCGA-EW-A1OV', 'TCGA-EW-A1OW', 'TCGA-EW-A1OX', 'TCGA-EW-A1OY', 'TCGA-EW-A1OZ', 'TCGA-EW-A1P0', 'TCGA-EW-A1P1', 'TCGA-EW-A1P3', 'TCGA-EW-A1P4', 'TCGA-EW-A1P5', 'TCGA-EW-A1P6', 'TCGA-EW-A1P7', 'TCGA-EW-A1P8', 'TCGA-EW-A1PA', 'TCGA-EW-A1PB', 'TCGA-EW-A1PC', 'TCGA-EW-A1PD', 'TCGA-EW-A1PE', 'TCGA-EW-A1PF', 'TCGA-EW-A1PG', 'TCGA-EW-A1PH', 'TCGA-EW-A2FR', 'TCGA-EW-A2FS', 'TCGA-EW-A2FV', 'TCGA-EW-A2FW', 'TCGA-EW-A3E8', 'TCGA-EW-A3U0', 'TCGA-EW-A423', 'TCGA-EW-A424', 'TCGA-EW-A6S9', 'TCGA-EW-A6SA', 'TCGA-EW-A6SB', 'TCGA-EW-A6SC', 'TCGA-EW-A6SD', 'TCGA-GI-A2C8', 'TCGA-GI-A2C8', 'TCGA-GI-A2C9', 'TCGA-GI-A2C9', 'TCGA-GM-A2D9', 'TCGA-GM-A2DA', 'TCGA-GM-A2DB', 'TCGA-GM-A2DC', 'TCGA-GM-A2DD', 'TCGA-GM-A2DF', 'TCGA-GM-A2DH', 'TCGA-GM-A2DI', 'TCGA-GM-A2DK', 'TCGA-GM-A2DL', 'TCGA-GM-A2DM', 'TCGA-GM-A2DN', 'TCGA-GM-A2DO', 'TCGA-GM-A3NW', 'TCGA-GM-A3NY', 'TCGA-GM-A3XG', 'TCGA-GM-A3XL', 'TCGA-GM-A3XN', 'TCGA-GM-A4E0', 'TCGA-GM-A5PV', 'TCGA-GM-A5PX', 'TCGA-HN-A2NL', 'TCGA-HN-A2OB', 'TCGA-JL-A3YW', 'TCGA-JL-A3YX', 'TCGA-LD-A66U', 'TCGA-LD-A74U', 'TCGA-LD-A7W5', 'TCGA-LD-A7W6', 'TCGA-LD-A9QF', 'TCGA-LL-A440', 'TCGA-LL-A441', 'TCGA-LL-A442', 'TCGA-LL-A50Y', 'TCGA-LL-A5YL', 'TCGA-LL-A5YM', 'TCGA-LL-A5YN', 'TCGA-LL-A5YO', 'TCGA-LL-A5YP', 'TCGA-LL-A6FP', 'TCGA-LL-A6FQ', 'TCGA-LL-A6FR', 'TCGA-LL-A73Y', 'TCGA-LL-A73Z', 'TCGA-LL-A740', 'TCGA-LL-A7SZ', 'TCGA-LL-A7T0', 'TCGA-LL-A8F5', 'TCGA-LL-A9Q3', 'TCGA-LQ-A4E4', 'TCGA-MS-A51U', 'TCGA-OK-A5Q2', 'TCGA-OL-A5D6', 'TCGA-OL-A5D7', 'TCGA-OL-A5D8', 'TCGA-OL-A5DA', 'TCGA-OL-A5RU', 'TCGA-OL-A5RV', 'TCGA-OL-A5RW', 'TCGA-OL-A5RX', 'TCGA-OL-A5RY', 'TCGA-OL-A5RZ', 'TCGA-OL-A5S0', 'TCGA-OL-A66H', 'TCGA-OL-A66I', 'TCGA-OL-A66J', 'TCGA-OL-A66K', 'TCGA-OL-A66L', 'TCGA-OL-A66N', 'TCGA-OL-A66O', 'TCGA-OL-A66P', 'TCGA-OL-A6VO', 'TCGA-OL-A6VQ', 'TCGA-OL-A6VR', 'TCGA-OL-A97C', 'TCGA-PE-A5DC', 'TCGA-PE-A5DD', 'TCGA-PE-A5DE', 'TCGA-PL-A8LV', 'TCGA-PL-A8LX', 'TCGA-PL-A8LY', 'TCGA-PL-A8LZ', 'TCGA-S3-A6ZF', 'TCGA-S3-A6ZG', 'TCGA-S3-A6ZH', 'TCGA-S3-AA0Z', 'TCGA-S3-AA10', 'TCGA-S3-AA11', 'TCGA-S3-AA12', 'TCGA-S3-AA14', 'TCGA-S3-AA15', 'TCGA-S3-AA17', 'TCGA-UL-AAZ6', 'TCGA-UU-A93S', 'TCGA-V7-A7HQ', 'TCGA-W8-A86G', 'TCGA-WT-AB41', 'TCGA-WT-AB44', 'TCGA-XX-A899', 'TCGA-XX-A89A', 'TCGA-Z7-A8R5', 'TCGA-Z7-A8R6'\""
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "case_list = \", \".join(\"'%s'\" % w for w in subtypes.case_barcode)\n",
    "case_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1282, 4)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>case_barcode</th>\n",
       "      <th>sample_barcode</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>sample_type_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-A2-A04P</td>\n",
       "      <td>TCGA-A2-A04P-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-AR-A0TP</td>\n",
       "      <td>TCGA-AR-A0TP-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-GM-A2DF</td>\n",
       "      <td>TCGA-GM-A2DF-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-D8-A141</td>\n",
       "      <td>TCGA-D8-A141-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode    sample_barcode sample_type     sample_type_name\n",
       "0  TCGA-A2-A04P  TCGA-A2-A04P-01A          01  Primary solid Tumor\n",
       "1  TCGA-AR-A0TP  TCGA-AR-A0TP-01A          01  Primary solid Tumor\n",
       "2  TCGA-GM-A2DF  TCGA-GM-A2DF-01A          01  Primary solid Tumor\n",
       "3  TCGA-BH-A0C0  TCGA-BH-A0C0-01A          01  Primary solid Tumor\n",
       "4  TCGA-D8-A141  TCGA-D8-A141-01A          01  Primary solid Tumor"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "client = bq.Client()\n",
    "biospecimen = 'isb-cgc.TCGA_bioclin_v0.Biospecimen'\n",
    "\n",
    "query = \"\"\"\\\n",
    "SELECT \n",
    "    case_barcode, sample_barcode, sample_type, sample_type_name\n",
    "FROM\n",
    "    `{}`\n",
    "WHERE\n",
    "    case_barcode IN ({}) AND sample_type IN ('01', '02', '06', '07', '11')\n",
    "\"\"\".format(biospecimen, case_list)\n",
    "\n",
    "samples = client.query(query).to_dataframe()\n",
    "\n",
    "print(samples.shape)\n",
    "\n",
    "samples.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Primary solid Tumor    1112\n",
       "Solid Tissue Normal     163\n",
       "Metastatic                7\n",
       "Name: sample_type_name, dtype: int64"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples.sample_type_name.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1282, 12)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>case_barcode</th>\n",
       "      <th>sample_barcode</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>sample_type_name</th>\n",
       "      <th>subtype</th>\n",
       "      <th>ER</th>\n",
       "      <th>PR</th>\n",
       "      <th>Her2_IHC</th>\n",
       "      <th>Her2_ISH</th>\n",
       "      <th>Her2</th>\n",
       "      <th>triple_negative</th>\n",
       "      <th>subtype_sub</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-A2-A04P</td>\n",
       "      <td>TCGA-A2-A04P-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Basal</td>\n",
       "      <td>Negative</td>\n",
       "      <td>Negative</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Negative</td>\n",
       "      <td>Negative</td>\n",
       "      <td>Yes</td>\n",
       "      <td>Basal-TN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-AR-A0TP</td>\n",
       "      <td>TCGA-AR-A0TP-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Basal</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Negative</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Basal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-GM-A2DF</td>\n",
       "      <td>TCGA-GM-A2DF-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Basal</td>\n",
       "      <td>Negative</td>\n",
       "      <td>Negative</td>\n",
       "      <td>1+</td>\n",
       "      <td>Negative</td>\n",
       "      <td>Negative</td>\n",
       "      <td>Yes</td>\n",
       "      <td>Basal-TN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>LumB</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>2+</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumB</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-D8-A141</td>\n",
       "      <td>TCGA-D8-A141-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>LumA</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>1+</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode    sample_barcode sample_type     sample_type_name subtype  \\\n",
       "0  TCGA-A2-A04P  TCGA-A2-A04P-01A          01  Primary solid Tumor   Basal   \n",
       "1  TCGA-AR-A0TP  TCGA-AR-A0TP-01A          01  Primary solid Tumor   Basal   \n",
       "2  TCGA-GM-A2DF  TCGA-GM-A2DF-01A          01  Primary solid Tumor   Basal   \n",
       "3  TCGA-BH-A0C0  TCGA-BH-A0C0-01A          01  Primary solid Tumor    LumB   \n",
       "4  TCGA-D8-A141  TCGA-D8-A141-01A          01  Primary solid Tumor    LumA   \n",
       "\n",
       "         ER        PR Her2_IHC  Her2_ISH      Her2 triple_negative subtype_sub  \n",
       "0  Negative  Negative      NaN  Negative  Negative             Yes    Basal-TN  \n",
       "1  Positive  Negative      NaN       NaN       NaN             NaN       Basal  \n",
       "2  Negative  Negative       1+  Negative  Negative             Yes    Basal-TN  \n",
       "3  Positive  Positive       2+  Positive       NaN             NaN        LumB  \n",
       "4  Positive  Positive       1+       NaN       NaN             NaN        LumA  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged = pd.merge(samples, subtypes.drop(['aliquot_barcode'], axis=1), how='left', \n",
    "                  on=['sample_barcode', 'case_barcode'])\n",
    "\n",
    "print(merged.shape)\n",
    "merged.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1282, 12)\n"
     ]
    }
   ],
   "source": [
    "print(merged.drop_duplicates().shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Primary solid Tumor    1112\n",
      "Solid Tissue Normal     163\n",
      "Metastatic                7\n",
      "Name: sample_type_name, dtype: int64\n",
      "\n",
      "\n",
      "LumA        581\n",
      "LumB        219\n",
      "Normal      143\n",
      "Basal       101\n",
      "Basal-TN     91\n",
      "Her2         82\n",
      "Name: subtype_sub, dtype: int64\n",
      "False    1217\n",
      "True       65\n",
      "Name: subtype_sub, dtype: int64\n"
     ]
    }
   ],
   "source": [
    "print(merged.sample_type_name.value_counts())\n",
    "print(\"\\n\")\n",
    "\n",
    "print(merged.subtype_sub.value_counts())\n",
    "print(merged.subtype_sub.isnull().value_counts())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Solid Tissue Normal    49\n",
       "Primary solid Tumor    15\n",
       "Name: sample_type_name, dtype: int64"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged.loc[merged.subtype.isnull(), \"sample_type_name\"].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "merged.to_csv(\"./metadata/subtype_metadata.tsv\", sep=\"\\t\", index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Hormone therapy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(480, 4)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>case_barcode</th>\n",
       "      <th>initial_response</th>\n",
       "      <th>recurrence_status</th>\n",
       "      <th>recurrence_log</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-5L-AAT0</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-5L-AAT1</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-5T-A9QA</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown neoplasm status</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-A1-A0SF</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-A1-A0SQ</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode initial_response recurrence_status           recurrence_log\n",
       "0  TCGA-5L-AAT0          Unknown               NaN                      NaN\n",
       "1  TCGA-5L-AAT1          Unknown               NaN                      NaN\n",
       "2  TCGA-5T-A9QA          Unknown           Unknown  Unknown neoplasm status\n",
       "3  TCGA-A1-A0SF          Unknown               NaN                      NaN\n",
       "4  TCGA-A1-A0SQ          Unknown               NaN                      NaN"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hormone = pd.read_table(\"metadata/hormone_response_recurrence.tsv\", sep=\"\\t\")\n",
    "\n",
    "print(hormone.shape)\n",
    "hormone.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(540, 4)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>case_barcode</th>\n",
       "      <th>sample_barcode</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>sample_type_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-D8-A141</td>\n",
       "      <td>TCGA-D8-A141-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-EW-A424</td>\n",
       "      <td>TCGA-EW-A424-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-AO-A12G</td>\n",
       "      <td>TCGA-AO-A12G-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-AC-A3QP</td>\n",
       "      <td>TCGA-AC-A3QP-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode    sample_barcode sample_type     sample_type_name\n",
       "0  TCGA-BH-A0C0  TCGA-BH-A0C0-01A          01  Primary solid Tumor\n",
       "1  TCGA-D8-A141  TCGA-D8-A141-01A          01  Primary solid Tumor\n",
       "2  TCGA-EW-A424  TCGA-EW-A424-01A          01  Primary solid Tumor\n",
       "3  TCGA-AO-A12G  TCGA-AO-A12G-01A          01  Primary solid Tumor\n",
       "4  TCGA-AC-A3QP  TCGA-AC-A3QP-01A          01  Primary solid Tumor"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "case_list = \", \".join(\"'%s'\" % w for w in hormone.case_barcode)\n",
    "\n",
    "client = bq.Client()\n",
    "biospecimen = 'isb-cgc.TCGA_bioclin_v0.Biospecimen'\n",
    "\n",
    "query = \"\"\"\\\n",
    "SELECT \n",
    "    case_barcode, sample_barcode, sample_type, sample_type_name\n",
    "FROM\n",
    "    `{}`\n",
    "WHERE\n",
    "    case_barcode IN ({}) AND sample_type IN ('01', '02', '06', '07', '11')\n",
    "\"\"\".format(biospecimen, case_list)\n",
    "\n",
    "samples = client.query(query).to_dataframe()\n",
    "\n",
    "print(samples.shape)\n",
    "\n",
    "samples.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Primary solid Tumor    486\n",
       "Solid Tissue Normal     53\n",
       "Metastatic               1\n",
       "Name: sample_type_name, dtype: int64"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples.sample_type_name.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(540, 7)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>case_barcode</th>\n",
       "      <th>sample_barcode</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>sample_type_name</th>\n",
       "      <th>initial_response</th>\n",
       "      <th>recurrence_status</th>\n",
       "      <th>recurrence_log</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-11A</td>\n",
       "      <td>11</td>\n",
       "      <td>Solid Tissue Normal</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-D8-A141</td>\n",
       "      <td>TCGA-D8-A141-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-EW-A424</td>\n",
       "      <td>TCGA-EW-A424-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-AO-A12G</td>\n",
       "      <td>TCGA-AO-A12G-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode    sample_barcode sample_type     sample_type_name  \\\n",
       "0  TCGA-BH-A0C0  TCGA-BH-A0C0-01A          01  Primary solid Tumor   \n",
       "1  TCGA-BH-A0C0  TCGA-BH-A0C0-11A          11  Solid Tissue Normal   \n",
       "2  TCGA-D8-A141  TCGA-D8-A141-01A          01  Primary solid Tumor   \n",
       "3  TCGA-EW-A424  TCGA-EW-A424-01A          01  Primary solid Tumor   \n",
       "4  TCGA-AO-A12G  TCGA-AO-A12G-01A          01  Primary solid Tumor   \n",
       "\n",
       "  initial_response recurrence_status  \\\n",
       "0          Unknown           Unknown   \n",
       "1          Unknown           Unknown   \n",
       "2          Unknown           Unknown   \n",
       "3          Unknown           Unknown   \n",
       "4          Unknown           Unknown   \n",
       "\n",
       "                                      recurrence_log  \n",
       "0  Alive tumor free, last follow-up within risky ...  \n",
       "1  Alive tumor free, last follow-up within risky ...  \n",
       "2  Alive tumor free, last follow-up within risky ...  \n",
       "3  Alive tumor free, last follow-up within risky ...  \n",
       "4  Alive tumor free, last follow-up within risky ...  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged = pd.merge(samples, hormone, how='inner', on='case_barcode')\n",
    "\n",
    "print(merged.shape)\n",
    "merged.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(540, 15)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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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>case_barcode</th>\n",
       "      <th>sample_barcode</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>sample_type_name</th>\n",
       "      <th>initial_response</th>\n",
       "      <th>recurrence_status</th>\n",
       "      <th>recurrence_log</th>\n",
       "      <th>subtype</th>\n",
       "      <th>ER</th>\n",
       "      <th>PR</th>\n",
       "      <th>Her2_IHC</th>\n",
       "      <th>Her2_ISH</th>\n",
       "      <th>Her2</th>\n",
       "      <th>triple_negative</th>\n",
       "      <th>subtype_sub</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "      <td>LumB</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>2+</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumB</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-BH-A0C0</td>\n",
       "      <td>TCGA-BH-A0C0-11A</td>\n",
       "      <td>11</td>\n",
       "      <td>Solid Tissue Normal</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "      <td>Normal</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>2+</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-D8-A141</td>\n",
       "      <td>TCGA-D8-A141-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "      <td>LumA</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>1+</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-EW-A424</td>\n",
       "      <td>TCGA-EW-A424-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "      <td>LumA</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TCGA-AO-A12G</td>\n",
       "      <td>TCGA-AO-A12G-01A</td>\n",
       "      <td>01</td>\n",
       "      <td>Primary solid Tumor</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Alive tumor free, last follow-up within risky ...</td>\n",
       "      <td>LumA</td>\n",
       "      <td>Positive</td>\n",
       "      <td>Positive</td>\n",
       "      <td>2+</td>\n",
       "      <td>Negative</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>LumA</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   case_barcode    sample_barcode sample_type     sample_type_name  \\\n",
       "0  TCGA-BH-A0C0  TCGA-BH-A0C0-01A          01  Primary solid Tumor   \n",
       "1  TCGA-BH-A0C0  TCGA-BH-A0C0-11A          11  Solid Tissue Normal   \n",
       "2  TCGA-D8-A141  TCGA-D8-A141-01A          01  Primary solid Tumor   \n",
       "3  TCGA-EW-A424  TCGA-EW-A424-01A          01  Primary solid Tumor   \n",
       "4  TCGA-AO-A12G  TCGA-AO-A12G-01A          01  Primary solid Tumor   \n",
       "\n",
       "  initial_response recurrence_status  \\\n",
       "0          Unknown           Unknown   \n",
       "1          Unknown           Unknown   \n",
       "2          Unknown           Unknown   \n",
       "3          Unknown           Unknown   \n",
       "4          Unknown           Unknown   \n",
       "\n",
       "                                      recurrence_log subtype        ER  \\\n",
       "0  Alive tumor free, last follow-up within risky ...    LumB  Positive   \n",
       "1  Alive tumor free, last follow-up within risky ...  Normal  Positive   \n",
       "2  Alive tumor free, last follow-up within risky ...    LumA  Positive   \n",
       "3  Alive tumor free, last follow-up within risky ...    LumA  Positive   \n",
       "4  Alive tumor free, last follow-up within risky ...    LumA  Positive   \n",
       "\n",
       "         PR Her2_IHC  Her2_ISH Her2 triple_negative subtype_sub  \n",
       "0  Positive       2+  Positive  NaN             NaN        LumB  \n",
       "1  Positive       2+  Positive  NaN             NaN      Normal  \n",
       "2  Positive       1+       NaN  NaN             NaN        LumA  \n",
       "3  Positive      NaN       NaN  NaN             NaN        LumA  \n",
       "4  Positive       2+  Negative  NaN             NaN        LumA  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hormone_metadata = pd.merge(merged, subtypes.drop(['aliquot_barcode'], axis=1), how='left', \n",
    "                            on=['sample_barcode', 'case_barcode'])\n",
    "print(hormone_metadata.shape)\n",
    "hormone_metadata.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>subtype_sub</th>\n",
       "      <th>Basal</th>\n",
       "      <th>Her2</th>\n",
       "      <th>LumA</th>\n",
       "      <th>LumB</th>\n",
       "      <th>Normal</th>\n",
       "      <th>All</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>initial_response</th>\n",
       "      <th></th>\n",
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Complete response</th>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>30</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>40</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Progressive/Stable</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Unknown</th>\n",
       "      <td>8</td>\n",
       "      <td>11</td>\n",
       "      <td>290</td>\n",
       "      <td>108</td>\n",
       "      <td>14</td>\n",
       "      <td>431</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>All</th>\n",
       "      <td>10</td>\n",
       "      <td>13</td>\n",
       "      <td>326</td>\n",
       "      <td>115</td>\n",
       "      <td>16</td>\n",
       "      <td>480</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "subtype_sub         Basal  Her2  LumA  LumB  Normal  All\n",
       "initial_response                                        \n",
       "Complete response       2     1    30     6       1   40\n",
       "Progressive/Stable      0     1     6     1       1    9\n",
       "Unknown                 8    11   290   108      14  431\n",
       "All                    10    13   326   115      16  480"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hormone_tumors = hormone_metadata.loc[hormone_metadata['sample_type']==\"01\"]\n",
    "pd.crosstab(hormone_tumors['initial_response'], hormone_tumors['subtype_sub'], margins=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Complete response: 2 Basal, 1 Normal-like\n",
    "- Progressive/Stable: 1 Normal-like"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "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>subtype_sub</th>\n",
       "      <th>Basal</th>\n",
       "      <th>Her2</th>\n",
       "      <th>LumA</th>\n",
       "      <th>LumB</th>\n",
       "      <th>Normal</th>\n",
       "      <th>All</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>recurrence_status</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Low risk</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Occured</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>28</td>\n",
       "      <td>11</td>\n",
       "      <td>1</td>\n",
       "      <td>42</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Unknown</th>\n",
       "      <td>9</td>\n",
       "      <td>12</td>\n",
       "      <td>283</td>\n",
       "      <td>104</td>\n",
       "      <td>15</td>\n",
       "      <td>423</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>All</th>\n",
       "      <td>10</td>\n",
       "      <td>13</td>\n",
       "      <td>319</td>\n",
       "      <td>115</td>\n",
       "      <td>16</td>\n",
       "      <td>473</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "subtype_sub        Basal  Her2  LumA  LumB  Normal  All\n",
       "recurrence_status                                      \n",
       "Low risk               0     0     8     0       0    8\n",
       "Occured                1     1    28    11       1   42\n",
       "Unknown                9    12   283   104      15  423\n",
       "All                   10    13   319   115      16  473"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.crosstab(hormone_tumors['recurrence_status'], hormone_tumors['subtype_sub'], margins=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Occured: 1 Basal, 1 Normal-like"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "hormone_metadata.to_csv(\"./metadata/hormone_metadata.tsv\", sep=\"\\t\", index=False)"
   ]
  }
 ],
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