| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Schizophrenia" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Schizophrenia/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Schizophrenia/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Schizophrenia/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Schizophrenia/cohort_info.json" | |
| # Since TCGA only contains cancer datasets, and schizophrenia is not a cancer, | |
| # we know there won't be suitable data - record unavailability and exit | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) | |
| # Return empty dataframes to avoid errors in subsequent code | |
| clinical_df = pd.DataFrame() | |
| genetic_df = pd.DataFrame() |