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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Chronic_Fatigue_Syndrome"
# Input paths
tcga_root_dir = "../DATA/TCGA"
# Output paths
out_data_file = "./output/preprocess/3/Chronic_Fatigue_Syndrome/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Chronic_Fatigue_Syndrome/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Chronic_Fatigue_Syndrome/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Chronic_Fatigue_Syndrome/cohort_info.json"
# Check available directories
available_dirs = os.listdir(tcga_root_dir)
available_dirs = [d for d in available_dirs if not d.startswith('.') and not d.endswith('.ipynb')]
# For cardiovascular disease, there is no directly matching cohort in TCGA
# Mark the trait as not available and exit
is_usable = validate_and_save_cohort_info(
is_final=False,
cohort="TCGA",
info_path=json_path,
is_gene_available=False,
is_trait_available=False
)
raise ValueError(f"No suitable TCGA cohort found for {trait}") |