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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Osteoarthritis"
# Input paths
tcga_root_dir = "../DATA/TCGA"
# Output paths
out_data_file = "./output/preprocess/3/Osteoarthritis/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Osteoarthritis/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Osteoarthritis/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Osteoarthritis/cohort_info.json"
# 1. Check if suitable directory exists for Osteoarthritis
# No suitable directory found in TCGA dataset
# Mark data as unavailable since no relevant cohort exists
is_gene_available = False
is_trait_available = False
# Record this information
validate_and_save_cohort_info(
is_final=False,
cohort="TCGA",
info_path=json_path,
is_gene_available=is_gene_available,
is_trait_available=is_trait_available
) |