CI_surv-features.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23240\\973629156.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n"
     ]
    }
   ],
   "source": [
    "\"\"\"Feature Data 01\"\"\"\n",
    "from lifelines.utils import concordance_index\n",
    "import pandas as pd\n",
    "\n",
    "ci_list=[]\n",
    "type_list=[]\n",
    "\n",
    "# Base: Survival data\n",
    "data_surv = pd.read_csv(filepath_or_buffer='./data/00-TCGA-CDR.csv', encoding='utf-8')\n",
    "\n",
    "# Extract tumor type in type\n",
    "tumor_types = data_surv['type'].astype('category').cat.categories.tolist()\n",
    "\n",
    "for i in range(len(tumor_types)):\n",
    "    # Extract matched tumor type datasets\n",
    "    data_tumor = data_surv.loc[data_surv['type'] == tumor_types[i]]\n",
    "    type_list.append(tumor_types[i])\n",
    "\n",
    "    # --------\n",
    "\n",
    "    # Feature data 01\n",
    "    f01_cnv = pd.read_csv(filepath_or_buffer='./data/01-CNV burden scores - seg_based_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
    "\n",
    "    # Remove last three characters in Sample column\n",
    "    f01_cnv['Sample'] = f01_cnv['Sample'].str[:-3]\n",
    "\n",
    "    # Extract feature rows by survival bcr_patient_barcode and remain main-feature\n",
    "    f01_cnv_bytype = f01_cnv[f01_cnv['Sample'].isin(data_tumor['bcr_patient_barcode'])]\n",
    "    f01_cnv_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
    "    f01_cnv_mfeature = f01_cnv_bytype.drop(columns=['n_segs', 'n_extrema'])\n",
    "\n",
    "    # ---------\n",
    "\n",
    "    # Preprocessing\n",
    "    # Common elements between survival - feature\n",
    "    common_elements = list(set(data_tumor['bcr_patient_barcode']).intersection(f01_cnv_mfeature['bcr_patient_barcode']))\n",
    "\n",
    "    # Extract common elements from both dataframes\n",
    "    data_tumor_common = data_tumor[data_tumor['bcr_patient_barcode'].isin(common_elements)]\n",
    "\n",
    "    # Concat two dataframes by bcr value\n",
    "    data_merged = pd.merge(data_tumor_common, f01_cnv_mfeature, on='bcr_patient_barcode')\n",
    "\n",
    "    data_cindex = data_merged.loc[:, ['bcr_patient_barcode', 'OS.time', 'OS', 'frac_altered']]\n",
    "\n",
    "    data_cindex.fillna(0, inplace=True)\n",
    "\n",
    "    # concordance_index must have same shape\n",
    "    c_index = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['frac_altered'])\n",
    "\n",
    "    ci_list.append(c_index)\n",
    "df_result = pd.DataFrame({'tumor_type': type_list, 'frac_altered': ci_list})\n",
    "df_result.to_csv(path_or_buf='./data/cindex_feature_01.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23132\\240499592.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n"
     ]
    }
   ],
   "source": [
    "\"\"\"Feature Data 02\"\"\"\n",
    "from lifelines.utils import concordance_index\n",
    "import pandas as pd\n",
    "\n",
    "ci_list=[]\n",
    "type_list=[]\n",
    "\n",
    "# Base: Survival data\n",
    "data_surv = pd.read_csv(filepath_or_buffer='./data/00-TCGA-CDR.csv', encoding='utf-8')\n",
    "\n",
    "# Extract tumor type in type\n",
    "tumor_types = data_surv['type'].astype('category').cat.categories.tolist()\n",
    "\n",
    "for i in range(len(tumor_types)):\n",
    "    # Extract matched tumor type datasets\n",
    "    data_tumor = data_surv.loc[data_surv['type'] == tumor_types[i]]\n",
    "    type_list.append(tumor_types[i])\n",
    "\n",
    "    # Feature data 02\n",
    "    f02_loh = pd.read_csv(filepath_or_buffer='./data/02-Aneuploidy and LOG Scores - ABSOLUTE_scores.tsv', sep='\\\\t', encoding='utf-8')\n",
    "\n",
    "    # Remove last three characters in Sample column\n",
    "    f02_loh['Sample'] = f02_loh['Sample'].str[:-3]\n",
    "\n",
    "    # Extract feature rows by survival bcr_patient_barcode and remain main-feature\n",
    "    f02_loh_bytype = f02_loh[f02_loh['Sample'].isin(data_tumor['bcr_patient_barcode'])]\n",
    "    f02_loh_bytype.rename(columns={'Sample':'bcr_patient_barcode'}, inplace=True)\n",
    "    f02_loh_mfeature = f02_loh_bytype.loc[:, ['bcr_patient_barcode', 'LOH_frac_altered']]\n",
    "    #f02_loh_mfeature.fillna(0, inplace=True)\n",
    "\n",
    "    # Preprocessing\n",
    "    # Common elements between survival - feature\n",
    "    common_elements = list(set(data_tumor['bcr_patient_barcode']).intersection(f02_loh_mfeature['bcr_patient_barcode']))\n",
    "\n",
    "    # Extract common elements from both dataframes\n",
    "    data_tumor_common = data_tumor[data_tumor['bcr_patient_barcode'].isin(common_elements)]\n",
    "\n",
    "    # Concat two dataframes by bcr value\n",
    "    data_merged = pd.merge(data_tumor_common, f02_loh_mfeature, on='bcr_patient_barcode')\n",
    "\n",
    "    data_cindex = data_merged.loc[:, ['bcr_patient_barcode', 'OS.time', 'OS', 'LOH_frac_altered']]\n",
    "\n",
    "    data_cindex.fillna(0, inplace=True)\n",
    "\n",
    "    # concordance_index must have same shape\n",
    "    c_index = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['LOH_frac_altered'])\n",
    "\n",
    "    ci_list.append(c_index)\n",
    "df_result = pd.DataFrame({'tumor_type': type_list, 'LOH_frac_altered': ci_list})\n",
    "df_result.to_csv(path_or_buf='./data/cindex_feature_02.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_17792\\2527922430.py:29: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n"
     ]
    }
   ],
   "source": [
    "\"\"\"Feature Data 03+04\"\"\"\n",
    "from lifelines.utils import concordance_index\n",
    "import pandas as pd\n",
    "\n",
    "ci_purity_ls=[]\n",
    "ci_ploidy_ls=[]\n",
    "type_list=[]\n",
    "\n",
    "# Base: Survival data\n",
    "data_surv = pd.read_csv(filepath_or_buffer='./data/00-TCGA-CDR.csv', encoding='utf-8')\n",
    "\n",
    "# Extract tumor type in type\n",
    "tumor_types = data_surv['type'].astype('category').cat.categories.tolist()\n",
    "\n",
    "for i in range(len(tumor_types)):\n",
    "    # Extract matched tumor type datasets\n",
    "    data_tumor = data_surv.loc[data_surv['type'] == tumor_types[i]]\n",
    "    type_list.append(tumor_types[i])\n",
    "\n",
    "    # Feature data 03: purity\n",
    "    # Feature data 04: ploidy\n",
    "    f34_puriploi = pd.read_csv(filepath_or_buffer='./data/03+04-ABSOLUTE ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt', sep='\\\\t', usecols=['array', 'purity', 'ploidy'], encoding='utf-8')\n",
    "\n",
    "    # Remove last three characters in Sample column\n",
    "    f34_puriploi['array'] = f34_puriploi['array'].str[:-3]\n",
    "\n",
    "    # Extract feature rows by survival bcr_patient_barcode and remain main-feature\n",
    "    f34_puriploi_bytype = f34_puriploi[f34_puriploi['array'].isin(data_tumor['bcr_patient_barcode'])]\n",
    "    f34_puriploi_bytype.rename(columns={'array':'bcr_patient_barcode'}, inplace=True)\n",
    "    f34_puriploi_mfeature = f34_puriploi_bytype.loc[:, ['bcr_patient_barcode', 'purity', 'ploidy']]\n",
    "    #f34_puriploi_mfeature.fillna(0, inplace=True)\n",
    "\n",
    "    # ---------\n",
    "    # Preprocessing\n",
    "    # Check common elements between survival - feature\n",
    "    common_elements = list(set(data_tumor['bcr_patient_barcode']).intersection(f34_puriploi_mfeature['bcr_patient_barcode']))\n",
    "\n",
    "    # Extract common elements from both dataframes\n",
    "    data_tumor_common = data_tumor[data_tumor['bcr_patient_barcode'].isin(common_elements)]\n",
    "\n",
    "    # Concat two dataframes by bcr value\n",
    "    data_merged = pd.merge(data_tumor_common, f34_puriploi_mfeature, on='bcr_patient_barcode')\n",
    "    data_cindex = data_merged.loc[:, ['bcr_patient_barcode', 'OS.time', 'OS', 'purity', 'ploidy']]\n",
    "    data_cindex.fillna(0, inplace=True)\n",
    "\n",
    "    # concordance_index must have same shape\n",
    "    # c-index for purity\n",
    "    ci_purity = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['purity'])\n",
    "    ci_purity_ls.append(ci_purity)\n",
    "\n",
    "    # c-index for ploidy\n",
    "    ci_ploidy = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['ploidy'])\n",
    "    ci_ploidy_ls.append(ci_ploidy)\n",
    "\n",
    "df_result = pd.DataFrame({'tumor_type':type_list, 'ci_purity':ci_purity_ls, 'ci_ploidy':ci_ploidy_ls})\n",
    "df_result.to_csv(path_or_buf='./data/cindex_feature_03+04.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:22: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_23660\\679245237.py:26: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n"
     ]
    }
   ],
   "source": [
    "\"\"\"Feature Data 05\"\"\"\n",
    "from lifelines.utils import concordance_index\n",
    "import pandas as pd\n",
    "\n",
    "ci_silent_ls=[]\n",
    "ci_nonsilent_ls=[]\n",
    "type_list=[]\n",
    "\n",
    "# Base: Survival data\n",
    "data_surv = pd.read_csv(filepath_or_buffer='./data/00-TCGA-CDR.csv', encoding='utf-8')\n",
    "\n",
    "# Extract tumor type in type\n",
    "tumor_types = data_surv['type'].astype('category').cat.categories.tolist()\n",
    "\n",
    "for i in range(len(tumor_types)):\n",
    "    # Extract matched tumor type datasets\n",
    "    data_tumor = data_surv.loc[data_surv['type'] == tumor_types[i]]\n",
    "    type_list.append(tumor_types[i])\n",
    "\n",
    "    # Feature data 05-1: Silent per Mb\n",
    "    # Feature data 05-2: Non-silent per Mb\n",
    "    f05_silent = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', usecols=['Patient_ID', 'Silent per Mb', 'Non-silent per Mb'], encoding='utf-8')\n",
    "\n",
    "    # Extract feature rows by survival bcr_patient_barcode and remain main-feature\n",
    "    f05_silent_bytype = f05_silent[f05_silent['Patient_ID'].isin(data_tumor['bcr_patient_barcode'])]\n",
    "    f05_silent_bytype.rename(columns={'Patient_ID':'bcr_patient_barcode'}, inplace=True)\n",
    "    f05_silent_mfeature = f05_silent_bytype.loc[:, ['bcr_patient_barcode', 'Silent per Mb', 'Non-silent per Mb']]\n",
    "\n",
    "    # ---------\n",
    "    # Preprocessing\n",
    "    # Check common elements between survival - feature\n",
    "    common_elements = list(set(data_tumor['bcr_patient_barcode']).intersection(f05_silent_mfeature['bcr_patient_barcode']))\n",
    "\n",
    "    # Extract common elements from both dataframes\n",
    "    data_tumor_common = data_tumor[data_tumor['bcr_patient_barcode'].isin(common_elements)]\n",
    "\n",
    "    # Concat two dataframes by bcr value\n",
    "    data_merged = pd.merge(data_tumor_common, f05_silent_mfeature, on='bcr_patient_barcode')\n",
    "    data_cindex = data_merged.loc[:, ['bcr_patient_barcode', 'OS.time', 'OS', 'Silent per Mb', 'Non-silent per Mb']]\n",
    "    data_cindex.fillna(0, inplace=True)\n",
    "\n",
    "    # concordance_index must have same shape\n",
    "    # c-index for purity\n",
    "    ci_silent = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['Silent per Mb'])\n",
    "    ci_silent_ls.append(ci_silent)\n",
    "\n",
    "    # c-index for ploidy\n",
    "    ci_nonsilent = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['Non-silent per Mb'])\n",
    "    ci_nonsilent_ls.append(ci_nonsilent)\n",
    "\n",
    "df_result = pd.DataFrame({'tumor_type':type_list, 'ci_silent':ci_silent_ls, 'ci_non-silent':ci_nonsilent_ls})\n",
    "df_result.to_csv(path_or_buf='./data/cindex_feature_05.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:20: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
      "  f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
      "C:\\Users\\user\\AppData\\Local\\Temp\\ipykernel_15964\\193930177.py:27: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n"
     ]
    }
   ],
   "source": [
    "\"\"\"Feature Data 06\"\"\"\n",
    "from lifelines.utils import concordance_index\n",
    "import pandas as pd\n",
    "\n",
    "ci_hrd_ls=[]\n",
    "type_list=[]\n",
    "\n",
    "# Base: Survival data\n",
    "data_surv = pd.read_csv(filepath_or_buffer='./data/00-TCGA-CDR.csv', encoding='utf-8')\n",
    "\n",
    "# Extract tumor type in type\n",
    "tumor_types = data_surv['type'].astype('category').cat.categories.tolist()\n",
    "\n",
    "for i in range(len(tumor_types)):\n",
    "    # Extract matched tumor type datasets\n",
    "    data_tumor = data_surv.loc[data_surv['type'] == tumor_types[i]]\n",
    "    type_list.append(tumor_types[i])\n",
    "\n",
    "    # Feature data 06: HRD\n",
    "    f06_hrd = pd.read_csv(filepath_or_buffer='./data/06-Homologous Repair Deficiency - TCGA.HRD_withSampleID.txt', sep='\\\\t', usecols=['sampleID', 'HRD'], encoding='utf-8')\n",
    "    \n",
    "    # Remove last three characters in Sample column\n",
    "    f06_hrd['sampleID'] = f06_hrd['sampleID'].str[:-3]\n",
    "\n",
    "    # Extract feature rows by survival bcr_patient_barcode and remain main-feature\n",
    "    f06_hrd_bytype = f06_hrd[f06_hrd['sampleID'].isin(data_tumor['bcr_patient_barcode'])]\n",
    "    f06_hrd_bytype.rename(columns={'sampleID':'bcr_patient_barcode'}, inplace=True)\n",
    "    f06_hrd_mfeature = f06_hrd_bytype.loc[:, ['bcr_patient_barcode', 'HRD']]\n",
    "\n",
    "    # ---------\n",
    "    # Preprocessing\n",
    "    # Check common elements between survival - feature\n",
    "    common_elements = list(set(data_tumor['bcr_patient_barcode']).intersection(f06_hrd_mfeature['bcr_patient_barcode']))\n",
    "\n",
    "    # Extract common elements from both dataframes\n",
    "    data_tumor_common = data_tumor[data_tumor['bcr_patient_barcode'].isin(common_elements)]\n",
    "\n",
    "    # Concat two dataframes by bcr value\n",
    "    data_merged = pd.merge(data_tumor_common, f06_hrd_mfeature, on='bcr_patient_barcode')\n",
    "    data_cindex = data_merged.loc[:, ['bcr_patient_barcode', 'OS.time', 'OS', 'HRD']]\n",
    "    data_cindex.fillna(0, inplace=True)\n",
    "\n",
    "    # concordance_index must have same shape\n",
    "    # c-index for HRD\n",
    "    ci_hrd = concordance_index(\n",
    "        event_times=data_cindex['OS.time'],\n",
    "        event_observed=data_cindex['OS'],\n",
    "        predicted_scores=-data_cindex['HRD'])\n",
    "    ci_hrd_ls.append(ci_hrd)\n",
    "\n",
    "df_result = pd.DataFrame({'tumor_type':type_list, 'ci_hrd':ci_hrd_ls})\n",
    "df_result.to_csv(path_or_buf='./data/cindex_feature_06.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# feature 마다 한번에 묶는것 비추\n",
    "# feature - survival 사이에 공통 데이터 갯수 차이가 조금 있음.\n",
    "# 따로 해서, c-index 구해야함."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Merge all\n",
    "import pandas as pd\n",
    "\n",
    "df_f1 = pd.read_csv(filepath_or_buffer='./data/cindex_feature_01.csv')\n",
    "df_f2 = pd.read_csv(filepath_or_buffer='./data/cindex_feature_02.csv')\n",
    "df_f3 = pd.read_csv(filepath_or_buffer='./data/cindex_feature_03+04.csv')\n",
    "df_f5 = pd.read_csv(filepath_or_buffer='./data/cindex_feature_05.csv')\n",
    "df_f6 = pd.read_csv(filepath_or_buffer='./data/cindex_feature_06.csv')\n",
    "\n",
    "df_merged12 = pd.merge(df_f1, df_f2, on='tumor_type')\n",
    "df_merged35 = pd.merge(df_f3, df_f5, on='tumor_type')\n",
    "df_merged1235 = pd.merge(df_merged12, df_merged35, on='tumor_type')\n",
    "df_merged = pd.merge(df_merged1235, df_f6, on='tumor_type')\n",
    "\n",
    "df_merged.to_csv(path_or_buf='./data/cindex_overall.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# predict_partial_hazard model\n",
    "from lifelines.utils import concordance_index\n",
    "from lifelines import CoxPHFitter\n",
    "\n",
    "# numeric data\n",
    "numeric_list = data_cindex.select_dtypes(include=[int, float]).columns.tolist()\n",
    "data_cindex_numeric = data_cindex.loc[:, numeric_list]\n",
    "\n",
    "#C-index\n",
    "# Survival Analysis에서 가장 많이 사용하는 정확도 지표입니다. 대상의 정확한 생존 시간을 평가하지 않고,\n",
    "# 대신 여러 대상의 생존 시간(또는 위험)을 상대적으로 비교합니다. 즉, 사망 순서를 잘 예측하는지 판단합니다.\n",
    "\n",
    "cph = CoxPHFitter().fit(data_cindex_numeric, duration_col='OS.time', event_col='OS')\n",
    "c_index = concordance_index(\n",
    "    event_times=data_cindex['OS.time'],\n",
    "    predicted_scores=-cph.predict_partial_hazard(data_cindex_numeric),\n",
    "    event_observed=data_cindex['OS'])\n",
    "cph.check_assumptions(data_cindex_numeric, p_value_threshold=0.05, show_plots=True)\n",
    "cph.print_summary()\n",
    "\n",
    "#adding a penalizer to the model,\n",
    "#ex: CoxPHFitter(penalizer=0.1).fit(…) until the model converges.\n",
    "#In the print_summary(), the coefficients that have high collinearity will have large (absolute) magnitude in the coefs column."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Feature data 05: Mutation Load\n",
    "f05_muload = pd.read_csv(filepath_or_buffer='./data/05-Mutation Load - mutation-load_updated.txt', sep='\\\\t', encoding='utf-8')\n",
    "\n",
    "# Drop unuse column\n",
    "f05_muload.drop(['Tumor_Sample_ID'], inplace=True)\n",
    "\n",
    "# ----------"
   ]
  }
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