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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Essential_Thrombocythemia"
# Input paths
tcga_root_dir = "../DATA/TCGA"
# Output paths
out_data_file = "./output/preprocess/3/Essential_Thrombocythemia/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Essential_Thrombocythemia/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Essential_Thrombocythemia/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Essential_Thrombocythemia/cohort_info.json"
# Review TCGA directories for Essential Thrombocythemia cohort
# LAML (Acute Myeloid Leukemia) is not directly relevant to Essential Thrombocythemia
print("No suitable TCGA cohort found for Essential Thrombocythemia")
# 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()