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# 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
) |