# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Migraine"

# Input paths
tcga_root_dir = "../DATA/TCGA"

# Output paths
out_data_file = "./output/preprocess/3/Migraine/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Migraine/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Migraine/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Migraine/cohort_info.json"

# Review the TCGA subdirectories for datasets relevant to Migraine
# No directory clearly related to migraine was found

# Record that this trait cannot be processed due to lack of suitable data
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path,
    is_gene_available=True, # TCGA has gene expression data
    is_trait_available=False # No suitable migraine data found
)