# Path Configuration from tools.preprocess import * # Processing context trait = "Psoriasis" # Input paths tcga_root_dir = "../DATA/TCGA" # Output paths out_data_file = "./output/preprocess/3/Psoriasis/TCGA.csv" out_gene_data_file = "./output/preprocess/3/Psoriasis/gene_data/TCGA.csv" out_clinical_data_file = "./output/preprocess/3/Psoriasis/clinical_data/TCGA.csv" json_path = "./output/preprocess/3/Psoriasis/cohort_info.json" # Review directories to find relevant cohort for Psoriasis cohorts = os.listdir(tcga_root_dir) cohorts = [d for d in cohorts if os.path.isdir(os.path.join(tcga_root_dir, d)) and d[0] != '.'] # No suitable cohort found for Psoriasis as it's not a cancer type covered by TCGA validate_and_save_cohort_info( is_final=False, cohort="TCGA", info_path=json_path, is_gene_available=False, is_trait_available=False )