output/preprocess/Eczema/code/TCGA.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Eczema"

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

# Output paths
out_data_file = "./output/z2/preprocess/Eczema/TCGA.csv"
out_gene_data_file = "./output/z2/preprocess/Eczema/gene_data/TCGA.csv"
out_clinical_data_file = "./output/z2/preprocess/Eczema/clinical_data/TCGA.csv"
json_path = "./output/z2/preprocess/Eczema/cohort_info.json"


# Step 1: Initial Data Loading
import os

# List available subdirectories in TCGA root directory
subdirectories = [
    '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)'
]

print(f"Looking for suitable cohort for trait: {trait}")
print("Available TCGA subdirectories:")
for subdir in subdirectories:
    print(f"  {subdir}")

# Eczema is an inflammatory skin condition, not a cancer
# None of the TCGA cancer cohorts are suitable for studying eczema
print(f"\nNo suitable TCGA cohort found for {trait}.")
print("TCGA focuses on cancer data, but eczema is an inflammatory skin condition, not a cancer.")
print("Skipping this trait for TCGA preprocessing.")

# Record that this trait is not available in TCGA
is_usable = validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path,
    is_gene_available=True,  # TCGA has gene data
    is_trait_available=False  # But not for eczema
)

print(f"Task completed. Trait {trait} is not suitable for TCGA analysis.")