| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Essential_Thrombocythemia" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Essential_Thrombocythemia/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Essential_Thrombocythemia/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Essential_Thrombocythemia/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Essential_Thrombocythemia/cohort_info.json" | |
| # Review TCGA directories for Essential Thrombocythemia cohort | |
| # LAML (Acute Myeloid Leukemia) is not directly relevant to Essential Thrombocythemia | |
| print("No suitable TCGA cohort found for Essential Thrombocythemia") | |
| # Mark task as completed by recording that gene/trait data is unavailable | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) | |
| # Exit preprocessing since no suitable data was found | |
| exit() |