# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Duchenne_Muscular_Dystrophy"

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

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

# Since DMD is a genetic disorder and not a cancer type, TCGA datasets are not suitable
# Record that trait data is not available and skip further processing
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path, 
    is_gene_available=True,  # TCGA would have gene data if we needed it
    is_trait_available=False  # No relevant trait data for DMD in TCGA cancer datasets
)