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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "461d7761",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T07:00:18.889703Z",
"iopub.status.busy": "2025-03-25T07:00:18.889550Z",
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"shell.execute_reply": "2025-03-25T07:00:19.055827Z"
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"outputs": [],
"source": [
"import sys\n",
"import os\n",
"sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '../..')))\n",
"\n",
"# Path Configuration\n",
"from tools.preprocess import *\n",
"\n",
"# Processing context\n",
"trait = \"Bone_Density\"\n",
"\n",
"# Input paths\n",
"tcga_root_dir = \"../../input/TCGA\"\n",
"\n",
"# Output paths\n",
"out_data_file = \"../../output/preprocess/Bone_Density/TCGA.csv\"\n",
"out_gene_data_file = \"../../output/preprocess/Bone_Density/gene_data/TCGA.csv\"\n",
"out_clinical_data_file = \"../../output/preprocess/Bone_Density/clinical_data/TCGA.csv\"\n",
"json_path = \"../../output/preprocess/Bone_Density/cohort_info.json\"\n"
]
},
{
"cell_type": "markdown",
"id": "b4e032e6",
"metadata": {},
"source": [
"### Step 1: Initial Data Loading"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "427fe1ea",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T07:00:19.057737Z",
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"shell.execute_reply": "2025-03-25T07:00:19.063799Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"No suitable directory found in TCGA for Bone_Density.\n",
"TCGA focuses on cancer types, not directly on bone density measurements.\n",
"Skipping this trait as recommended in the guidelines.\n"
]
},
{
"data": {
"text/plain": [
"False"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import os\n",
"import pandas as pd\n",
"\n",
"# 1. Find the most relevant directory for Bone Density\n",
"subdirectories = os.listdir(tcga_root_dir)\n",
"target_trait = trait.lower().replace(\"_\", \" \") # Convert to lowercase for case-insensitive matching\n",
"\n",
"# Words related to bone density that might appear in directory names\n",
"bone_related_terms = [\"bone\", \"density\", \"osteoporosis\", \"skeletal\", \"osseous\"]\n",
"\n",
"# First try direct matches\n",
"matched_dir = None\n",
"for subdir in subdirectories:\n",
" subdir_lower = subdir.lower()\n",
" # Check if any bone-related term is in the directory name\n",
" if any(term in subdir_lower for term in bone_related_terms):\n",
" matched_dir = subdir\n",
" break\n",
"\n",
"# If no direct match found, look specifically for Sarcoma as it may include bone sarcomas\n",
"if not matched_dir:\n",
" for subdir in subdirectories:\n",
" if \"sarcoma_(sarc)\" in subdir.lower():\n",
" matched_dir = subdir\n",
" break\n",
"\n",
"# No suitable directory found - we should skip this trait\n",
"print(f\"No suitable directory found in TCGA for {trait}.\")\n",
"print(\"TCGA focuses on cancer types, not directly on bone density measurements.\")\n",
"print(\"Skipping this trait as recommended in the guidelines.\")\n",
"\n",
"validate_and_save_cohort_info(\n",
" is_final=False,\n",
" cohort=\"TCGA\",\n",
" info_path=json_path,\n",
" is_gene_available=False,\n",
" is_trait_available=False\n",
")"
]
}
],
"metadata": {
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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