2.01.ipynb

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     "text": [
      "              Gene Symbol  TCGA-69-8253-01A  TCGA-69-8255-01A  \\\n",
      "0      ENSG00000008128.21                 0                 0   \n",
      "1      ENSG00000008130.14                 0                 0   \n",
      "2      ENSG00000067606.14                 0                 0   \n",
      "3      ENSG00000078369.16                 0                 0   \n",
      "4      ENSG00000078808.15                 0                 0   \n",
      "...                   ...               ...               ...   \n",
      "19724   ENSG00000277745.1                 0                 0   \n",
      "19725   ENSG00000277858.1                 0                 0   \n",
      "19726  ENSG00000124333.13                 0                 0   \n",
      "19727  ENSG00000124334.15                 0                 0   \n",
      "19728   ENSG00000168939.9                 0                 0   \n",
      "\n",
      "       TCGA-86-8278-01A  TCGA-97-8179-01A  TCGA-83-5908-01A  TCGA-69-8254-01A  \\\n",
      "0                     1                 0                 0                 0   \n",
      "1                     1                 0                 0                 0   \n",
      "2                     1                 0                 0                 0   \n",
      "3                     1                 0                 0                 0   \n",
      "4                     1                 0                 0                 0   \n",
      "...                 ...               ...               ...               ...   \n",
      "19724                 0                 0                 0                 0   \n",
      "19725                 0                 0                 0                 0   \n",
      "19726                 0                 0                 0                 0   \n",
      "19727                 0                 0                 0                 0   \n",
      "19728                 0                 0                 0                 0   \n",
      "\n",
      "       TCGA-97-8171-01A  TCGA-97-8172-01A  TCGA-97-8175-01A  ...  \\\n",
      "0                     0                 0                 0  ...   \n",
      "1                     0                 0                 0  ...   \n",
      "2                     0                 0                 0  ...   \n",
      "3                     0                 0                 0  ...   \n",
      "4                     0                 0                 0  ...   \n",
      "...                 ...               ...               ...  ...   \n",
      "19724                 0                 0                 0  ...   \n",
      "19725                 0                 0                 0  ...   \n",
      "19726                 0                 0                 0  ...   \n",
      "19727                 0                 0                 0  ...   \n",
      "19728                 0                 0                 0  ...   \n",
      "\n",
      "       TCGA-44-6147-01B  TCGA-44-6147-01A.1  TCGA-44-2662-01A.2  \\\n",
      "0                     0                   0                   0   \n",
      "1                     0                   0                   0   \n",
      "2                     0                   0                   0   \n",
      "3                     0                   0                   0   \n",
      "4                     0                   0                   0   \n",
      "...                 ...                 ...                 ...   \n",
      "19724                 0                   0                   0   \n",
      "19725                 0                   0                   0   \n",
      "19726                 0                   0                   0   \n",
      "19727                 0                   0                   0   \n",
      "19728                 0                   0                   0   \n",
      "\n",
      "       TCGA-44-2662-01B  TCGA-44-2665-01B  TCGA-44-2665-01A.2  \\\n",
      "0                     0                 1                   1   \n",
      "1                     0                 1                   1   \n",
      "2                     0                 1                   1   \n",
      "3                     0                 1                   1   \n",
      "4                     0                 1                   1   \n",
      "...                 ...               ...                 ...   \n",
      "19724                 0                 0                   0   \n",
      "19725                 0                 0                   0   \n",
      "19726                 0                 0                   0   \n",
      "19727                 0                 0                   0   \n",
      "19728                 0                 0                   0   \n",
      "\n",
      "       TCGA-44-2666-01B  TCGA-44-2666-01A.1  TCGA-44-2668-01B  \\\n",
      "0                     1                   0                 1   \n",
      "1                     1                   0                 1   \n",
      "2                     1                   0                 1   \n",
      "3                     1                   0                 1   \n",
      "4                     1                   0                 1   \n",
      "...                 ...                 ...               ...   \n",
      "19724                 0                   0                 0   \n",
      "19725                 0                   0                 0   \n",
      "19726                 0                   0                 0   \n",
      "19727                 0                   0                 0   \n",
      "19728                 0                   0                 0   \n",
      "\n",
      "       TCGA-44-2668-01A.2  \n",
      "0                       0  \n",
      "1                       0  \n",
      "2                       0  \n",
      "3                       0  \n",
      "4                       0  \n",
      "...                   ...  \n",
      "19724                   0  \n",
      "19725                   0  \n",
      "19726                   0  \n",
      "19727                   0  \n",
      "19728                   0  \n",
      "\n",
      "[19729 rows x 556 columns]\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "# 读取数据\n",
    "file_path = 'datasets\\TCGA-LUAD.gistic.tsv'\n",
    "data = pd.read_csv(file_path, sep='\\t')\n",
    "\n",
    "print(data)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import requests\n",
    "import gzip\n",
    "import shutil\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "# 样本类型代码映射\n",
    "type_mapping = {\n",
    "    '01': 1,  # Primary Solid Tumor\n",
    "    '02': 1,  # Recurrent Solid Tumor\n",
    "    '03': 1,  # Primary Blood Derived Cancer - Peripheral Blood\n",
    "    '04': 1,  # Recurrent Blood Derived Cancer - Bone Marrow\n",
    "    '05': 1,  # Additional - New Primary\n",
    "    '06': 1,  # Metastatic\n",
    "    '07': 1,  # Additional Metastatic\n",
    "    '08': 1,  # Human Tumor Original Cells\n",
    "    '09': 1,  # Primary Blood Derived Cancer - Bone Marrow\n",
    "    '10': 0,  # Blood Derived Normal\n",
    "    '11': 0,  # Solid Tissue Normal\n",
    "    '12': 0,  # Buccal Cell Normal\n",
    "    '13': 0,  # EBV Immortalized Normal\n",
    "    '14': 0,  # Bone Marrow Normal\n",
    "    '15': 0,  # sample type 15\n",
    "    '16': 0,  # sample type 16\n",
    "    '20': 0,  # Control Analyte\n",
    "    '40': 1,  # Recurrent Blood Derived Cancer - Peripheral Blood\n",
    "    '50': 0,  # Cell Lines\n",
    "    '60': 0,  # Primary Xenograft Tissue\n",
    "    '61': 0,  # Cell Line Derived Xenograft Tissue\n",
    "    '99': 0   # sample type 99\n",
    "}\n",
    "\n",
    "def process_data(file_path):\n",
    "    # 读取数据\n",
    "    df = pd.read_csv(file_path, sep='\\t')\n",
    "    \n",
    "    # 提取样本编号\n",
    "    def get_status(sample_id):\n",
    "        sample_id_str = str(sample_id).strip()  # 确保样本编号是字符串，并去除空格\n",
    "        if len(sample_id_str) < 5:  # 检查样本编号长度\n",
    "            return 'Unknown'  # 样本编号格式不正确\n",
    "        sample_type_code = sample_id_str.split('-')[-1][:2]  # 提取样本类型代码\n",
    "        return type_mapping.get(sample_type_code, 'Unknown')  # 查找对应的状态\n",
    "    \n",
    "    # 创建状态行\n",
    "    status_row = {}\n",
    "    for column in df.columns[1:]:  # 跳过第一列 'Gene Symbol'\n",
    "        sample_id = df[column].iloc[0]  # 取该列的样本编号\n",
    "        status_row[column] = get_status(sample_id)\n",
    "    \n",
    "    # 将状态行添加到数据框中\n",
    "    status_df = pd.DataFrame(status_row, index=['Status']).T  # 转置数据框\n",
    "    df_with_status = pd.concat([df, status_df], axis=0)\n",
    "\n",
    "    return df_with_status\n",
    "\n",
    "def save_processed_data(df, output_path):\n",
    "    # 保存处理后的数据\n",
    "    df.to_pickle(output_path)\n",
    "\n",
    "def find_healthy_samples(df):\n",
    "    # 查找健康样本\n",
    "    healthy_samples_df = df[df['Status'] == 0]\n",
    "    return healthy_samples_df\n",
    "\n",
    "# 使用示例\n",
    "file_path = 'datasets/TCGA-OV.gistic.tsv'\n",
    "output_pkl_path = './datasets/TCGA-OV.gistic_processed.pkl'\n",
    "\n",
    "# 处理数据\n",
    "processed_df = process_data(file_path)\n",
    "\n",
    "# 保存处理后的数据\n",
    "save_processed_data(processed_df, output_pkl_path)\n"
   ]
  }
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