| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Hypertension" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Hypertension/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Hypertension/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Hypertension/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Hypertension/cohort_info.json" | |
| # 1. Check if any subdirectory is relevant to Hypertension | |
| subdirectories = os.listdir(tcga_root_dir) | |
| subdirectories = [d for d in subdirectories if os.path.isdir(os.path.join(tcga_root_dir, d))] | |
| # No suitable directory exists in TCGA for Hypertension since it's a cancer database | |
| is_gene_available = False # No relevant gene expression data | |
| is_trait_available = False # No relevant trait data | |
| # Record that this trait cannot be studied with TCGA data | |
| 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 | |
| ) |