def main(argv=sys.argv[1:]):
parser = argparse.ArgumentParser(
description="Produce a pedigree drawing in PDF format "
"from a pedigree file with layout coordinates.",
conflict_handler="resolve",
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('--verbose', '-V', action='count', default=0)
FamiliesLoader.cli_arguments(parser)
parser.add_argument(
"--output",
"-o",
metavar="o",
help="the output filename file",
default="output.pdf",
)
parser.add_argument(
"--mode",
type=str,
default="report",
dest="mode",
help="mode of drawing; supported modes are `families` and `report`; "
"defaults: `report`",
)
argv = parser.parse_args(argv)
if argv.verbose == 1:
logging.basicConfig(level=logging.WARNING)
elif argv.verbose == 2:
logging.basicConfig(level=logging.INFO)
elif argv.verbose >= 3:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.WARNING)
logging.getLogger("matplotlib").setLevel(logging.WARNING)
filename, params = FamiliesLoader.parse_cli_arguments(argv)
families_loader = FamiliesLoader(filename, **params)
families = families_loader.load()
mode = argv.mode
assert mode in ("families", "report")
print("mode:", mode)
if mode == "report":
generator = draw_families_report(families)
else:
generator = draw_families(families)
with PDFLayoutDrawer(argv.output) as pdf_drawer:
for fig in generator:
pdf_drawer.savefig(fig)
plt.close(fig)
def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument('--verbose', '-V', action='count', default=0)
FamiliesLoader.cli_arguments(parser)
parser.add_argument(
"-o",
"--output",
dest="output_filename",
help="output families parquet filename "
"(default is [basename(families_filename).parquet])",
)
parser.add_argument(
"--partition-description",
"--pd",
help="input partition description filename",
)
parser.add_argument(
"--study-id",
type=str,
default=None,
dest="study_id",
metavar="<study id>",
help="Study ID. "
"If none specified, the basename of families filename is used to "
"construct study id [default: basename(families filename)]",
)
argv = parser.parse_args(argv)
if argv.verbose == 1:
logging.basicConfig(level=logging.WARNING)
elif argv.verbose == 2:
logging.basicConfig(level=logging.INFO)
elif argv.verbose >= 3:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.ERROR)
filename, params = FamiliesLoader.parse_cli_arguments(argv)
if argv.study_id is not None:
study_id = argv.study_id
else:
study_id, _ = os.path.splitext(os.path.basename(filename))
loader = FamiliesLoader(filename, **params)
families = loader.load()
if argv.partition_description:
partition_description = ParquetPartitionDescriptor.from_config(
argv.partition_description
)
if partition_description.family_bin_size > 0:
families = partition_description \
.add_family_bins_to_families(families)
if not argv.output_filename:
output_filename, _ = os.path.splitext(os.path.basename(filename))
output_filename = f"{output_filename}.parquet"
else:
output_filename = argv.output_filename
ParquetManager.families_to_parquet(families, output_filename)
def main(argv, gpf_instance=None):
if gpf_instance is None:
gpf_instance = GPFInstance()
parser = argparse.ArgumentParser()
parser.add_argument('--verbose', '-V', action='count', default=0)
FamiliesLoader.cli_arguments(parser)
VcfLoader.cli_arguments(parser, options_only=True)
parser.add_argument(
"-o",
"--output",
dest="output_filename",
help="output families parquet filename "
"(default is [basename(families_filename).ped])",
)
parser.add_argument(
"--partition-description",
"--pd",
help="input partition description filename",
)
parser.add_argument(
"--vcf-files",
type=str,
nargs="+",
metavar="<VCF filename>",
help="VCF file to import",
)
argv = parser.parse_args(argv)
if argv.verbose == 1:
logging.basicConfig(level=logging.WARNING)
elif argv.verbose == 2:
logging.basicConfig(level=logging.INFO)
elif argv.verbose >= 3:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.WARNING)
filename, params = FamiliesLoader.parse_cli_arguments(argv)
logger.info(F"PED PARAMS: {params}")
loader = FamiliesLoader(filename, **params)
families = loader.load()
if argv.partition_description:
partition_description = ParquetPartitionDescriptor.from_config(
argv.partition_description)
families = partition_description.add_family_bins_to_families(families)
variants_filenames, variants_params = \
VcfLoader.parse_cli_arguments(argv)
if variants_filenames:
assert variants_filenames is not None
variants_loader = VcfLoader(
families,
variants_filenames,
params=variants_params,
genome=gpf_instance.genomes_db.get_genome(),
)
families = variants_loader.families
if families.broken_families:
for family_id, family in families.broken_families.items():
if not family.has_members():
del families[family_id]
logger.warning(
f"family {family_id} does not contain sequenced members "
f"and is removed from the pedigree: {family}")
if not argv.output_filename:
output_filename, _ = os.path.splitext(os.path.basename(filename))
output_filename = f"{output_filename}.ped"
else:
output_filename = argv.output_filename
FamiliesLoader.save_pedigree(families, output_filename)
