| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Obstructive_sleep_apnea" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Obstructive_sleep_apnea/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Obstructive_sleep_apnea/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Obstructive_sleep_apnea/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Obstructive_sleep_apnea/cohort_info.json" | |
| # Check for OSA-related directory in TCGA | |
| # Since TCGA is focused on cancer, no directory is related to OSA | |
| is_gene_available = False | |
| is_trait_available = False | |
| # Mark task as completed and save info about data unavailability | |
| 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 | |
| ) |