# Generate a PharmCAT outside call file from a StellarPGx allele file
from argparse import ArgumentParser
from pathlib import Path
import pandas as pd
import shutil


def parse_file(infile):
    """
    Generate a PharmCAT outside call file from a StellarPGx allele file
    (also save input file to data/)

    Args:
        infile (str): StellarPGx allele file
    """
    assert infile.endswith(".alleles")
    gene = infile.split("_")[-1][:-8].upper()
    infile = Path(infile)
    assert infile.exists()

    stem =  infile.stem.replace(".deduped", "")

    shutil.copy(infile, "data/" + stem + ".alleles")
    outfile = "data/" + stem + ".tsv"

    with open(infile, "r") as f:
        lines = f.read().split("\n")
    result = ""
    likely = ""
    for i, line in enumerate(lines):
        if line.strip() == "Result:":
            result = lines[i+1]
        elif line.strip() == "Likely background alleles:":
            likely = lines[i+1]
    if result.startswith("Possible"):
        diplotype = likely
    else:
        diplotype = result
    pd.DataFrame([[gene, diplotype]]).to_csv(outfile, sep="\t", index=False, header=False)



def main():
    parser = ArgumentParser(description="StellarPGx Output Parser")
    parser.add_argument('input_file', type=str, help="StellarPGx allele file")
    args = parser.parse_args()
    parse_file(args.input_file)


if __name__ == '__main__':
    main()