# Path Configuration | |
from tools.preprocess import * | |
# Processing context | |
trait = "Heart_rate" | |
# Input paths | |
tcga_root_dir = "../DATA/TCGA" | |
# Output paths | |
out_data_file = "./output/preprocess/3/Heart_rate/TCGA.csv" | |
out_gene_data_file = "./output/preprocess/3/Heart_rate/gene_data/TCGA.csv" | |
out_clinical_data_file = "./output/preprocess/3/Heart_rate/clinical_data/TCGA.csv" | |
json_path = "./output/preprocess/3/Heart_rate/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('.')] | |
# Review cohort directories for heart rate related data | |
heart_cohorts = [d for d in tcga_subdirs if any(word in d.lower() for word in ['heart', 'cardiac', 'cardiovascular'])] | |
# No suitable cohort found for heart rate - 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 | |
) |