| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Atrial_Fibrillation" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/1/Atrial_Fibrillation/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/1/Atrial_Fibrillation/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/1/Atrial_Fibrillation/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/1/Atrial_Fibrillation/cohort_info.json" | |
| import os | |
| # Step 1: Check directories in tcga_root_dir for anything relevant to "Atrial_Fibrillation" | |
| dir_list = os.listdir(tcga_root_dir) | |
| matching_dir = None | |
| # We'll perform a simple match check (case-insensitive) | |
| # If we had any subdirectory name containing "atrial" or "fibrillation", we would choose it. | |
| for d in dir_list: | |
| if "atrial" in d.lower() or "fibrillation" in d.lower(): | |
| matching_dir = d | |
| break | |
| # If no suitable directory is found, mark trait as skipped | |
| if matching_dir is None: | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) | |
| else: | |
| # Normally we'd proceed with file loading, but per instructions, | |
| # no directory matches the trait. Thus this block won't execute. | |
| pass |