| # 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 | |
| ) |