# Path Configuration | |
from tools.preprocess import * | |
# Processing context | |
trait = "Fibromyalgia" | |
# Input paths | |
tcga_root_dir = "../DATA/TCGA" | |
# Output paths | |
out_data_file = "./output/preprocess/3/Fibromyalgia/TCGA.csv" | |
out_gene_data_file = "./output/preprocess/3/Fibromyalgia/gene_data/TCGA.csv" | |
out_clinical_data_file = "./output/preprocess/3/Fibromyalgia/clinical_data/TCGA.csv" | |
json_path = "./output/preprocess/3/Fibromyalgia/cohort_info.json" | |
# Review TCGA directories for Fibromyalgia cohort | |
print("No suitable TCGA cohort found for Fibromyalgia") | |
# Mark task as completed by recording that gene/trait data is unavailable | |
validate_and_save_cohort_info( | |
is_final=False, | |
cohort="TCGA", | |
info_path=json_path, | |
is_gene_available=False, | |
is_trait_available=False | |
) | |
# Exit preprocessing since no suitable data was found | |
exit() |