# Path Configuration | |
from tools.preprocess import * | |
# Processing context | |
trait = "Sjögrens_Syndrome" | |
# Input paths | |
tcga_root_dir = "../DATA/TCGA" | |
# Output paths | |
out_data_file = "./output/preprocess/3/Sjögrens_Syndrome/TCGA.csv" | |
out_gene_data_file = "./output/preprocess/3/Sjögrens_Syndrome/gene_data/TCGA.csv" | |
out_clinical_data_file = "./output/preprocess/3/Sjögrens_Syndrome/clinical_data/TCGA.csv" | |
json_path = "./output/preprocess/3/Sjögrens_Syndrome/cohort_info.json" | |
# Review available TCGA cohorts to find matches for Sjögren's Syndrome | |
cohorts = [d for d in os.listdir(tcga_root_dir) if os.path.isdir(os.path.join(tcga_root_dir, d))] | |
# No suitable cohort exists for Sjögren's Syndrome | |
# Mark this trait as not available using validate_and_save_cohort_info | |
validate_and_save_cohort_info( | |
is_final=False, | |
cohort="TCGA", | |
info_path=json_path, | |
is_gene_available=False, | |
is_trait_available=False | |
) |