# 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
)