| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Substance_Use_Disorder" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Substance_Use_Disorder/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Substance_Use_Disorder/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Substance_Use_Disorder/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Substance_Use_Disorder/cohort_info.json" | |
| # Get list of available cohorts | |
| available_cohorts = [d for d in os.listdir(tcga_root_dir) | |
| if os.path.isdir(os.path.join(tcga_root_dir, d)) and not d.startswith('.')] | |
| # Check for directories related to substance use disorder | |
| substance_related_dirs = [d for d in available_cohorts | |
| if any(term in d.lower() for term in ['substance', 'addiction', 'drug', 'alcohol'])] | |
| # Since no relevant directories found, record this and end processing | |
| clinical_df = None | |
| genetic_df = None | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort='TCGA', | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) |