Source code for dae.tools.simple_family2pedigree

#!/usr/bin/env python
import argparse
import os
import sys

from dae.pedigrees.loader import FamiliesLoader




def parse_cli_arguments(argv=sys.argv[1:]):
    parser = argparse.ArgumentParser(
        description="simple import of new study data",
        conflict_handler="resolve",
        formatter_class=argparse.RawDescriptionHelpFormatter,
    )

    parser.add_argument(
        "family_filename",
        type=str,
        metavar="<family filename>",
        help="families file in simple families format",
    )
    parser.add_argument(
        "--id",
        type=str,
        metavar="<study ID>",
        dest="id",
        help="Unique study ID to use. "
        "If not specified the basename of the family file is used "
        "for study ID",
    )

    parser.add_argument(
        "-o",
        "--out",
        type=str,
        default=None,
        dest="output",
        metavar="<output filename>",
        help="output filename. If not specified the output filename"
        "is constructed from <study id>.ped",
    )
    parser_args = parser.parse_args(argv)
    return parser_args





def main(argv):
    args = parse_cli_arguments(argv[1:])
    if args.id is not None:
        study_id = args.id
    else:
        study_id, _ = os.path.splitext(os.path.basename(args.family_filename))

    if args.output is None:
        output = f"{study_id}.ped"
    else:
        output = args.output

    fam_df = FamiliesLoader.load_simple_family_file(args.family_filename)
    FamiliesLoader.save_pedigree(fam_df, output)



if __name__ == "__main__":
    main(sys.argv)