| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Hypertrophic_Cardiomyopathy" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Hypertrophic_Cardiomyopathy/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Hypertrophic_Cardiomyopathy/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Hypertrophic_Cardiomyopathy/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Hypertrophic_Cardiomyopathy/cohort_info.json" | |
| # Get subdirectories from TCGA root directory | |
| tcga_subdirs = os.listdir(tcga_root_dir) | |
| tcga_subdirs = [d for d in tcga_subdirs if not d.startswith('.')] | |
| # No suitable cohort exists for HDL deficiency in TCGA cancer datasets | |
| # Record this and end processing | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=True, | |
| is_trait_available=False | |
| ) |