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dd19378 |
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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Werner_Syndrome"
# Input paths
tcga_root_dir = "../DATA/TCGA"
# Output paths
out_data_file = "./output/preprocess/3/Werner_Syndrome/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Werner_Syndrome/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Werner_Syndrome/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Werner_Syndrome/cohort_info.json"
# Review all cohort directories
cohorts = os.listdir(tcga_root_dir)
cohorts = [c for c in cohorts if not c.startswith('.') and not c.endswith('.ipynb')]
# No suitable cohort for Von Willebrand Disease in TCGA dataset
# Mark task as completed with no available data
validate_and_save_cohort_info(
is_final=False,
cohort="TCGA",
info_path=json_path,
is_gene_available=False,
is_trait_available=False
) |