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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "High-Density_Lipoprotein_Deficiency"
# Input paths
tcga_root_dir = "../DATA/TCGA"
# Output paths
out_data_file = "./output/preprocess/3/High-Density_Lipoprotein_Deficiency/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/High-Density_Lipoprotein_Deficiency/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/High-Density_Lipoprotein_Deficiency/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/High-Density_Lipoprotein_Deficiency/cohort_info.json"
# Get subdirectories from TCGA root directory
tcga_subdirs = os.listdir(tcga_root_dir)
tcga_subdirs = [d for d in tcga_subdirs if not d.startswith('.')]
# No suitable cohort exists for HDL deficiency in TCGA cancer datasets
# Record this and end processing
validate_and_save_cohort_info(
is_final=False,
cohort="TCGA",
info_path=json_path,
is_gene_available=True,
is_trait_available=False
) |