#!/usr/bin/env python
import argparse
import os
import sys
from dae.pedigrees.loader import FamiliesLoader
[docs]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
[docs]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)