| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Vitamin_D_Levels" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Vitamin_D_Levels/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Vitamin_D_Levels/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Vitamin_D_Levels/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Vitamin_D_Levels/cohort_info.json" | |
| # Review all cohort directories | |
| cohorts = os.listdir(tcga_root_dir) | |
| cohorts = [c for c in cohorts if not c.startswith('.') and not c.endswith('.ipynb')] | |
| # No suitable cohort found for Vitamin D Levels | |
| cohort = "TCGA" # Use TCGA as cohort name for metadata recording | |
| # Record that no suitable data is available and mark task as complete | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort=cohort, | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) |