| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Asthma" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Asthma/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Asthma/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Asthma/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Asthma/cohort_info.json" | |
| # Review available cohorts for asthma relevance | |
| tcga_dirs = os.listdir(tcga_root_dir) | |
| # Filter out non-directory files | |
| tcga_dirs = [d for d in tcga_dirs if os.path.isdir(os.path.join(tcga_root_dir, d))] | |
| # For asthma trait, none of the TCGA cancer cohorts are directly relevant | |
| print(f"No suitable TCGA cancer cohort was found for the trait: {trait}") | |
| # Save cohort info to mark this trait as completed | |
| _ = validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) | |
| # Exit preprocessing as no suitable data exists | |
| clinical_df = None | |
| genetic_df = None |