| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Cystic_Fibrosis" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Cystic_Fibrosis/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Cystic_Fibrosis/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Cystic_Fibrosis/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Cystic_Fibrosis/cohort_info.json" | |
| # Review subdirectories and check if any matches cystic fibrosis phenotype | |
| cohorts = [d for d in os.listdir(tcga_root_dir) if os.path.isdir(os.path.join(tcga_root_dir, d))] | |
| # No suitable cohort exists for cystic fibrosis in TCGA | |
| # Record this in metadata and exit | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) |