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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Gaucher_Disease"
# Input paths
tcga_root_dir = "../DATA/TCGA"
# Output paths
out_data_file = "./output/preprocess/3/Gaucher_Disease/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Gaucher_Disease/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Gaucher_Disease/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Gaucher_Disease/cohort_info.json"
# No relevant cohort exists for Gaucher Disease in TCGA dataset
is_gene_available = False # No gene expression data available
is_trait_available = False # No trait data available
# Record that this trait needs to be skipped due to lack of relevant data
validate_and_save_cohort_info(
is_final=False,
cohort="TCGA",
info_path=json_path,
is_gene_available=is_gene_available,
is_trait_available=is_trait_available
)
# Exit further processing since no suitable data exists
print("No suitable TCGA cohort found for Gaucher Disease. Skipping this trait.") |