| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "HIV_Resistance" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/HIV_Resistance/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/HIV_Resistance/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/HIV_Resistance/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/HIV_Resistance/cohort_info.json" | |
| # Review available cohorts and check for HIV resistance relevance | |
| available_cohorts = os.listdir(tcga_root_dir) | |
| cohorts = [c for c in available_cohorts if not c.startswith('.') and not c.endswith('.ipynb')] | |
| # No suitable cohort found for HIV resistance in TCGA cancer datasets | |
| is_gene_available = False | |
| is_trait_available = False | |
| # 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 | |
| ) |