pred_ld.py

import time
import os
import argparse
import pandas as pd
import pred_ld_functions
start = time.time()


def main():


    # Parse arguments
    global imp_snp_list
    imp_snp_list = []
    version = '1.0.0'
    print("---------------------------------------------------------------------------------")
    print("PRED-LD : GWAS Summary Statistics Imputation")
    print("Version " + version + "; January 2025")
    print("Copyright (C) 2025 Pantelis Bagos")
    print("Freely distributed under the GNU General Public Licence (GPLv3)")
    print("---------------------------------------------------------------------------------")

    parser = argparse.ArgumentParser(description="Process data in chunks.")
    parser.add_argument('--file-path', type=str, required=True, help='Input file path')
    parser.add_argument('--r2threshold', type=float, required=True, help='R2 threshold')
    parser.add_argument('--pop', type=str, required=True, help='Population')

    parser.add_argument('--maf', type=float, required=True, help='MAF input value')
    parser.add_argument('--ref', type=str, required=False, help='LD Reference files (Pheno_Scanner, TOP_LD, Hap_Map or all_panels)',default='all_panels')
    parser.add_argument('--imp_list', type=str, required=False,
                        help='A filename to define SNPs to impute (each SNP has a new line, no header)')

    args = parser.parse_args()

    # Accessing arguments using dashes (convert dashes to underscores)
    file_path = args.file_path
    r2threshold = args.r2threshold
    population = args.pop
    maf_input = args.maf
    ref_file = args.ref
    imp_snp_list_path = args.imp_list

    if imp_snp_list_path != None:
        imp_snp_list = list(pd.read_csv(imp_snp_list_path, header=None)[0])
    # chromosome = args.chrom

    if not os.path.exists(file_path):
        print(f"Error: File {file_path} not found.")
        return

    pred_ld_functions.process_data(file_path, r2threshold, population, maf_input, ref_file,imp_snp_list)


if __name__ == "__main__":
    main()

end = time.time()
print(f"Total Time: {end - start} seconds")