# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Intellectual_Disability"

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

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

# Get subdirectories from TCGA root directory
tcga_subdirs = os.listdir(tcga_root_dir)
tcga_subdirs = [d for d in tcga_subdirs if not d.startswith('.')]

# Review available subdirectories for insomnia-related cohorts
# No suitable cohort found - all are cancer specific and not related to sleep disorders
print(f"No suitable TCGA cohort found for {trait}.")
print("Available cohorts are cancer-specific and do not contain relevant data for sleep disorders.")

# Record that this trait should be skipped due to lack of suitable data
is_gene_available = False
is_trait_available = False
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)