extract_patient-ids.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 患者ID抽出"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Study ID</th>\n",
       "      <th>Patient ID</th>\n",
       "      <th>Sample ID</th>\n",
       "      <th>Age at Diagnosis</th>\n",
       "      <th>Type of Breast Surgery</th>\n",
       "      <th>Cancer Type</th>\n",
       "      <th>Cancer Type Detailed</th>\n",
       "      <th>Cellularity</th>\n",
       "      <th>Chemotherapy</th>\n",
       "      <th>Pam50 + Claudin-low subtype</th>\n",
       "      <th>...</th>\n",
       "      <th>Relapse Free Status (Months)</th>\n",
       "      <th>Relapse Free Status</th>\n",
       "      <th>Number of Samples Per Patient</th>\n",
       "      <th>Sample Type</th>\n",
       "      <th>Sex</th>\n",
       "      <th>3-Gene classifier subtype</th>\n",
       "      <th>TMB (nonsynonymous)</th>\n",
       "      <th>Tumor Size</th>\n",
       "      <th>Tumor Stage</th>\n",
       "      <th>Patient's Vital Status</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>brca_metabric</td>\n",
       "      <td>MB-0000</td>\n",
       "      <td>MB-0000</td>\n",
       "      <td>75.65</td>\n",
       "      <td>MASTECTOMY</td>\n",
       "      <td>Breast Cancer</td>\n",
       "      <td>Breast Invasive Ductal Carcinoma</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NO</td>\n",
       "      <td>claudin-low</td>\n",
       "      <td>...</td>\n",
       "      <td>138.65</td>\n",
       "      <td>0:Not Recurred</td>\n",
       "      <td>1</td>\n",
       "      <td>Primary</td>\n",
       "      <td>Female</td>\n",
       "      <td>ER-/HER2-</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>22.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>Living</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>brca_metabric</td>\n",
       "      <td>MB-0002</td>\n",
       "      <td>MB-0002</td>\n",
       "      <td>43.19</td>\n",
       "      <td>BREAST CONSERVING</td>\n",
       "      <td>Breast Cancer</td>\n",
       "      <td>Breast Invasive Ductal Carcinoma</td>\n",
       "      <td>High</td>\n",
       "      <td>NO</td>\n",
       "      <td>LumA</td>\n",
       "      <td>...</td>\n",
       "      <td>83.52</td>\n",
       "      <td>0:Not Recurred</td>\n",
       "      <td>1</td>\n",
       "      <td>Primary</td>\n",
       "      <td>Female</td>\n",
       "      <td>ER+/HER2- High Prolif</td>\n",
       "      <td>2.615035</td>\n",
       "      <td>10.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>Living</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>brca_metabric</td>\n",
       "      <td>MB-0005</td>\n",
       "      <td>MB-0005</td>\n",
       "      <td>48.87</td>\n",
       "      <td>MASTECTOMY</td>\n",
       "      <td>Breast Cancer</td>\n",
       "      <td>Breast Invasive Ductal Carcinoma</td>\n",
       "      <td>High</td>\n",
       "      <td>YES</td>\n",
       "      <td>LumB</td>\n",
       "      <td>...</td>\n",
       "      <td>151.28</td>\n",
       "      <td>1:Recurred</td>\n",
       "      <td>1</td>\n",
       "      <td>Primary</td>\n",
       "      <td>Female</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.615035</td>\n",
       "      <td>15.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>Died of Disease</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>brca_metabric</td>\n",
       "      <td>MB-0006</td>\n",
       "      <td>MB-0006</td>\n",
       "      <td>47.68</td>\n",
       "      <td>MASTECTOMY</td>\n",
       "      <td>Breast Cancer</td>\n",
       "      <td>Breast Mixed Ductal and Lobular Carcinoma</td>\n",
       "      <td>Moderate</td>\n",
       "      <td>YES</td>\n",
       "      <td>LumB</td>\n",
       "      <td>...</td>\n",
       "      <td>162.76</td>\n",
       "      <td>0:Not Recurred</td>\n",
       "      <td>1</td>\n",
       "      <td>Primary</td>\n",
       "      <td>Female</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.307518</td>\n",
       "      <td>25.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>Living</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>brca_metabric</td>\n",
       "      <td>MB-0008</td>\n",
       "      <td>MB-0008</td>\n",
       "      <td>76.97</td>\n",
       "      <td>MASTECTOMY</td>\n",
       "      <td>Breast Cancer</td>\n",
       "      <td>Breast Mixed Ductal and Lobular Carcinoma</td>\n",
       "      <td>High</td>\n",
       "      <td>YES</td>\n",
       "      <td>LumB</td>\n",
       "      <td>...</td>\n",
       "      <td>18.55</td>\n",
       "      <td>1:Recurred</td>\n",
       "      <td>1</td>\n",
       "      <td>Primary</td>\n",
       "      <td>Female</td>\n",
       "      <td>ER+/HER2- High Prolif</td>\n",
       "      <td>2.615035</td>\n",
       "      <td>40.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>Died of Disease</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 39 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Study ID Patient ID Sample ID  Age at Diagnosis  \\\n",
       "0  brca_metabric    MB-0000   MB-0000             75.65   \n",
       "1  brca_metabric    MB-0002   MB-0002             43.19   \n",
       "2  brca_metabric    MB-0005   MB-0005             48.87   \n",
       "3  brca_metabric    MB-0006   MB-0006             47.68   \n",
       "4  brca_metabric    MB-0008   MB-0008             76.97   \n",
       "\n",
       "  Type of Breast Surgery    Cancer Type  \\\n",
       "0             MASTECTOMY  Breast Cancer   \n",
       "1      BREAST CONSERVING  Breast Cancer   \n",
       "2             MASTECTOMY  Breast Cancer   \n",
       "3             MASTECTOMY  Breast Cancer   \n",
       "4             MASTECTOMY  Breast Cancer   \n",
       "\n",
       "                        Cancer Type Detailed Cellularity Chemotherapy  \\\n",
       "0           Breast Invasive Ductal Carcinoma         NaN           NO   \n",
       "1           Breast Invasive Ductal Carcinoma        High           NO   \n",
       "2           Breast Invasive Ductal Carcinoma        High          YES   \n",
       "3  Breast Mixed Ductal and Lobular Carcinoma    Moderate          YES   \n",
       "4  Breast Mixed Ductal and Lobular Carcinoma        High          YES   \n",
       "\n",
       "  Pam50 + Claudin-low subtype  ...  Relapse Free Status (Months)  \\\n",
       "0                 claudin-low  ...                        138.65   \n",
       "1                        LumA  ...                         83.52   \n",
       "2                        LumB  ...                        151.28   \n",
       "3                        LumB  ...                        162.76   \n",
       "4                        LumB  ...                         18.55   \n",
       "\n",
       "  Relapse Free Status Number of Samples Per Patient  Sample Type     Sex  \\\n",
       "0      0:Not Recurred                             1      Primary  Female   \n",
       "1      0:Not Recurred                             1      Primary  Female   \n",
       "2          1:Recurred                             1      Primary  Female   \n",
       "3      0:Not Recurred                             1      Primary  Female   \n",
       "4          1:Recurred                             1      Primary  Female   \n",
       "\n",
       "  3-Gene classifier subtype TMB (nonsynonymous) Tumor Size Tumor Stage  \\\n",
       "0                 ER-/HER2-            0.000000       22.0         2.0   \n",
       "1     ER+/HER2- High Prolif            2.615035       10.0         1.0   \n",
       "2                       NaN            2.615035       15.0         2.0   \n",
       "3                       NaN            1.307518       25.0         2.0   \n",
       "4     ER+/HER2- High Prolif            2.615035       40.0         2.0   \n",
       "\n",
       "  Patient's Vital Status  \n",
       "0                 Living  \n",
       "1                 Living  \n",
       "2        Died of Disease  \n",
       "3                 Living  \n",
       "4        Died of Disease  \n",
       "\n",
       "[5 rows x 39 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df=pd.read_table('./results/raw/brca_metabric_clinical_data.tsv')\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['MB-0000', 'MB-0002', 'MB-0005', ..., 'MTS-T2430', 'MTS-T2431',\n",
       "       'MTS-T2432'], dtype=object)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "patient_ids=df['Patient ID']\n",
    "patient_ids.to_csv('patient_ids.csv',index=False)"
   ]
  }
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