from argparse import ArgumentParser
import pandas as pd
import os


def combine(sample):
    files = os.listdir("data/")
    dfs = []
    for f in files:
        f = "data/" + f
        if f.startswith(sample + "_cyp") and f.endswith(".tsv"):
            dfs.append(pd.read_csv(f, sep="\t", header=None))
            os.unlink(f)
    df = pd.concat(dfs, ignore_index=True).dropna()
    df.to_csv(f"{sample}_outside_call.tsv", sep="\t", index=False, header=False)


def main():
    parser = ArgumentParser(description="Combine StellarPGx Output")
    parser.add_argument('sample', type=str, help="StellarPGx allele file prefix")
    args = parser.parse_args()
    combine(args.sample.replace("_calls", ""))

if __name__ == '__main__':
    main()