main_config_snp_parallel_automated_mut_rate.py

import subprocess
import argparse
import yaml

def main():

    parser = argparse.ArgumentParser(description="Run commands in series with automatic mutation rate configuration.")
    parser.add_argument("-t", required=True, help="Type parameter for the second command.")
    parser.add_argument("-f", required=True, help="File path for the input probability matrix.")
    parser.add_argument("-p", type=float, required=True, help="Probability parameter for the first command.")
    parser.add_argument("-m", type=int, default=1000, help="Number of histories used to estimate mut rate.")
    parser.add_argument("-l", type=int, required=True, help="Length parameter for the second command.")
    args = parser.parse_args()

    # Run the first command

    print("\n")
    print("AUTOMATED ESTIMATION OF MUTATION RATE\n")
    print("Using gaussian approximation of tree length distribution to obtain mutation rate..\n")
    cmd1 = [
        "python", "scr/main_est_mutation_rate_oneshot.py",
        "-a", "gauss",
        "-p", str(args.p),
        "-m", str(args.m),
        "-t", args.t,
        "-f", args.f,
        "-rs", "1"
    ]
    result1 = subprocess.run(cmd1, capture_output=True, text=True, check=True)

    # Parse the output of the first command
    output_lines = result1.stdout.strip().split("\n")
    mut_rate, error_bar = map(float, output_lines[-1].split())

    print(f"Estimated mutation rate: {mut_rate}\n")
    print(f"Estimate error in the fraction of invariant sites: {error_bar}\n")


    # Run the second command
    print("GENERATING THE SNP CONFIGURATION")
    cmd2 = [
        "caffeinate", "recopops", "snps",
        "-t", args.t,
        "-f", args.f,
        "-rs", "1",
        "-u", str(mut_rate),
        "-v", "0",
        "-l", str(args.l)
    ]
    subprocess.run(cmd2, check=True)
    print("\n")

if __name__ == "__main__":
    main()