# Path Configuration | |
from tools.preprocess import * | |
# Processing context | |
trait = "Psoriasis" | |
# Input paths | |
tcga_root_dir = "../DATA/TCGA" | |
# Output paths | |
out_data_file = "./output/preprocess/3/Psoriasis/TCGA.csv" | |
out_gene_data_file = "./output/preprocess/3/Psoriasis/gene_data/TCGA.csv" | |
out_clinical_data_file = "./output/preprocess/3/Psoriasis/clinical_data/TCGA.csv" | |
json_path = "./output/preprocess/3/Psoriasis/cohort_info.json" | |
# Review directories to find relevant cohort for Psoriasis | |
cohorts = os.listdir(tcga_root_dir) | |
cohorts = [d for d in cohorts if os.path.isdir(os.path.join(tcga_root_dir, d)) and d[0] != '.'] | |
# No suitable cohort found for Psoriasis as it's not a cancer type covered by TCGA | |
validate_and_save_cohort_info( | |
is_final=False, | |
cohort="TCGA", | |
info_path=json_path, | |
is_gene_available=False, | |
is_trait_available=False | |
) |