| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Generalized_Anxiety_Disorder" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Generalized_Anxiety_Disorder/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Generalized_Anxiety_Disorder/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Generalized_Anxiety_Disorder/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Generalized_Anxiety_Disorder/cohort_info.json" | |
| # No relevant cohort exists for Generalized Anxiety Disorder in TCGA dataset | |
| is_gene_available = False # No gene expression data available | |
| is_trait_available = False # No trait data available | |
| # Record that this trait needs to be skipped due to lack of relevant 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 | |
| ) | |
| # Exit further processing since no suitable data exists | |
| print("No suitable TCGA cohort found for Generalized Anxiety Disorder. Skipping this trait.") |