# Path Configuration | |
from tools.preprocess import * | |
# Processing context | |
trait = "Angelman_Syndrome" | |
# Input paths | |
tcga_root_dir = "../DATA/TCGA" | |
# Output paths | |
out_data_file = "./output/preprocess/3/Angelman_Syndrome/TCGA.csv" | |
out_gene_data_file = "./output/preprocess/3/Angelman_Syndrome/gene_data/TCGA.csv" | |
out_clinical_data_file = "./output/preprocess/3/Angelman_Syndrome/clinical_data/TCGA.csv" | |
json_path = "./output/preprocess/3/Angelman_Syndrome/cohort_info.json" | |
# 1. Review subdirectories and find no suitable match for ALS | |
# No cohort in TCGA matches or overlaps with amyotrophic lateral sclerosis | |
# Mark trait as unavailable and skip further processing | |
validate_and_save_cohort_info( | |
is_final=False, | |
cohort="TCGA", | |
info_path=json_path, | |
is_gene_available=False, | |
is_trait_available=False | |
) |