| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Insomnia" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Insomnia/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Insomnia/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Insomnia/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Insomnia/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('.')] | |
| # Review available subdirectories for insomnia-related cohorts | |
| # No suitable cohort found - all are cancer specific and not related to sleep disorders | |
| print(f"No suitable TCGA cohort found for {trait}.") | |
| print("Available cohorts are cancer-specific and do not contain relevant data for sleep disorders.") | |
| # Record that this trait should be skipped due to lack of suitable data | |
| is_gene_available = False | |
| is_trait_available = False | |
| validate_and_save_cohort_info(is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=is_gene_available, | |
| is_trait_available=is_trait_available) |