p3/preprocess/Post-Traumatic_Stress_Disorder/code/TCGA.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Post-Traumatic_Stress_Disorder"

# Input paths
tcga_root_dir = "../DATA/TCGA"

# Output paths
out_data_file = "./output/preprocess/3/Post-Traumatic_Stress_Disorder/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Post-Traumatic_Stress_Disorder/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Post-Traumatic_Stress_Disorder/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Post-Traumatic_Stress_Disorder/cohort_info.json"

# 1. Check TCGA directories for PTSD-related data
all_dirs = ['CrawlData.ipynb', '.DS_Store', 'TCGA_lower_grade_glioma_and_glioblastoma_(GBMLGG)', 'TCGA_Uterine_Carcinosarcoma_(UCS)', 'TCGA_Thyroid_Cancer_(THCA)', 'TCGA_Thymoma_(THYM)', 'TCGA_Testicular_Cancer_(TGCT)', 'TCGA_Stomach_Cancer_(STAD)', 'TCGA_Sarcoma_(SARC)', 'TCGA_Rectal_Cancer_(READ)', 'TCGA_Prostate_Cancer_(PRAD)', 'TCGA_Pheochromocytoma_Paraganglioma_(PCPG)', 'TCGA_Pancreatic_Cancer_(PAAD)', 'TCGA_Ovarian_Cancer_(OV)', 'TCGA_Ocular_melanomas_(UVM)', 'TCGA_Mesothelioma_(MESO)', 'TCGA_Melanoma_(SKCM)', 'TCGA_Lung_Squamous_Cell_Carcinoma_(LUSC)', 'TCGA_Lung_Cancer_(LUNG)', 'TCGA_Lung_Adenocarcinoma_(LUAD)', 'TCGA_Lower_Grade_Glioma_(LGG)', 'TCGA_Liver_Cancer_(LIHC)', 'TCGA_Large_Bcell_Lymphoma_(DLBC)', 'TCGA_Kidney_Papillary_Cell_Carcinoma_(KIRP)', 'TCGA_Kidney_Clear_Cell_Carcinoma_(KIRC)', 'TCGA_Kidney_Chromophobe_(KICH)', 'TCGA_Head_and_Neck_Cancer_(HNSC)', 'TCGA_Glioblastoma_(GBM)', 'TCGA_Esophageal_Cancer_(ESCA)', 'TCGA_Endometrioid_Cancer_(UCEC)', 'TCGA_Colon_and_Rectal_Cancer_(COADREAD)', 'TCGA_Colon_Cancer_(COAD)', 'TCGA_Cervical_Cancer_(CESC)', 'TCGA_Breast_Cancer_(BRCA)', 'TCGA_Bladder_Cancer_(BLCA)', 'TCGA_Bile_Duct_Cancer_(CHOL)', 'TCGA_Adrenocortical_Cancer_(ACC)', 'TCGA_Acute_Myeloid_Leukemia_(LAML)']

# No directories contain PTSD-related data since TCGA is a cancer database
is_gene_available = False
is_trait_available = False

# Record that no suitable data is available
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path,
    is_gene_available=is_gene_available,
    is_trait_available=is_trait_available
)