Python FamiliesLoader.load_simple_family_file Examples

Example #1

File: simple_family2pedigree.py Project: iossifovlab/gpf

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)

Example #2

File: dae_conftests.py Project: iossifovlab/gpf

    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