| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Ankylosing_Spondylitis" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Ankylosing_Spondylitis/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Ankylosing_Spondylitis/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Ankylosing_Spondylitis/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Ankylosing_Spondylitis/cohort_info.json" | |
| # 1. Review subdirectories | |
| # No cohort in TCGA matches or overlaps with Ankylosing Spondylitis (AS), which is an | |
| # autoimmune condition rather than a cancer type. The available cancer cohorts are not | |
| # relevant for studying this inflammatory arthritis condition. | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) |