# Path Configuration
from tools.preprocess import *

# Processing context
trait = "HIV_Resistance"

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

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

# Review available cohorts and check for HIV resistance relevance
available_cohorts = os.listdir(tcga_root_dir)
cohorts = [c for c in available_cohorts if not c.startswith('.') and not c.endswith('.ipynb')]

# No suitable cohort found for HIV resistance in TCGA cancer datasets
is_gene_available = False  
is_trait_available = False

# Record that this trait cannot be studied with TCGA 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
)