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 = "{study_id}.ped".format(study_id=study_id)
else:
output = args.output
fam_df = FamiliesLoader.load_simple_family_file(args.family_filename)
FamiliesLoader.save_pedigree(fam_df, output)
def builder(path, region=None):
config = config_dae(path)
ped_df = FamiliesLoader.load_simple_family_file(
dae_transmitted_config.family_filename)
dae = DaeTransmittedLoader(
config.dae.summary_filename,
config.dae.toomany_filename,
ped_df,
region=region,
genome=genome_2013,
)
return dae