| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Anorexia_Nervosa" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Anorexia_Nervosa/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Anorexia_Nervosa/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Anorexia_Nervosa/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Anorexia_Nervosa/cohort_info.json" | |
| # Review the provided TCGA subdirectories | |
| # No suitable TCGA cohort found for Anorexia Nervosa as TCGA only contains cancer-related | |
| # datasets, while Anorexia Nervosa is an eating disorder. None of the available cancer | |
| # cohorts are relevant for studying this psychiatric/metabolic condition. | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) |