def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: postprocess_variants does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
with genomics_io.make_ref_reader(FLAGS.ref) as reader:
contigs = reader.contigs
paths = io_utils.maybe_generate_sharded_filenames(FLAGS.infile)
with tempfile.NamedTemporaryFile() as temp:
postprocess_variants_lib.process_single_sites_tfrecords(
contigs, paths, temp.name)
# Read one CallVariantsOutput record and extract the sample name from it.
# Note that this assumes that all CallVariantsOutput protos in the infile
# contain a single VariantCall within their constituent Variant proto, and
# that the call_set_name is identical in each of the records.
record = next(
io_utils.read_tfrecords(
paths[0],
proto=deepvariant_pb2.CallVariantsOutput,
max_records=1))
sample_name = _extract_single_sample_name(record)
write_call_variants_output_to_vcf(
contigs=contigs,
input_sorted_tfrecord_path=temp.name,
output_vcf_path=FLAGS.outfile,
qual_filter=FLAGS.qual_filter,
multi_allelic_qual_filter=FLAGS.multi_allelic_qual_filter,
sample_name=sample_name)
def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: make_examples does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
hts_verbose.set(hts_verbose.htsLogLevel[FLAGS.hts_logging_level])
# Give htslib authentication access to GCS.
htslib_gcp_oauth.init()
# Set up options; may do I/O.
options = default_options(add_flags=True, flags=FLAGS)
# Check arguments that apply to any mode.
if not options.reference_filename:
errors.log_and_raise('ref argument is required.',
errors.CommandLineError)
if not options.reads_filename:
errors.log_and_raise('reads argument is required.',
errors.CommandLineError)
if not options.examples_filename:
errors.log_and_raise('examples argument is required.',
errors.CommandLineError)
if options.n_cores != 1:
errors.log_and_raise(
'Currently only supports n_cores == 1 but got {}.'.format(
options.n_cores), errors.CommandLineError)
# Check for argument issues specific to train mode.
if in_training_mode(options):
if not options.truth_variants_filename:
errors.log_and_raise(
'truth_variants is required when in training mode.',
errors.CommandLineError)
if not options.confident_regions_filename:
errors.log_and_raise(
'confident_regions is required when in training mode.',
errors.CommandLineError)
if options.gvcf_filename:
errors.log_and_raise('gvcf is not allowed in training mode.',
errors.CommandLineError)
else:
# Check for argument issues specific to calling mode.
if options.variant_caller_options.sample_name == _UNKNOWN_SAMPLE:
errors.log_and_raise(
'sample_name must be specified in calling mode.',
errors.CommandLineError)
# Run!
make_examples_runner(options)
def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: call_variants does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
# Give htslib authentication access to GCS.
htslib_gcp_oauth.init()
model = modeling.get_model(FLAGS.model_name)
call_variants(examples_filename=FLAGS.examples,
checkpoint_path=FLAGS.checkpoint,
model=model,
execution_hardware=FLAGS.execution_hardware,
output_file=FLAGS.outfile,
max_batches=FLAGS.max_batches,
batch_size=FLAGS.batch_size)
def test_clean_commandline_error_exit_clean_exit(self, exc_type,
exit_value):
with mock.patch.object(sys, 'exit') as mock_exit:
with errors.clean_commandline_error_exit(exit_value=exit_value):
raise exc_type()
mock_exit.assert_called_once_with(exit_value)
def test_clean_commandline_error_exit_raise_non_allowed(
self, exc_type, msg):
with self.assertRaisesRegexp(exc_type, msg):
with errors.clean_commandline_error_exit():
raise exc_type(msg)
def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: postprocess_variants does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
if (not FLAGS.nonvariant_site_tfrecord_path) != (
not FLAGS.gvcf_outfile):
errors.log_and_raise(
'gVCF creation requires both nonvariant_site_tfrecord_path and '
'gvcf_outfile flags to be set.', errors.CommandLineError)
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
with genomics_io.make_ref_reader(FLAGS.ref) as reader:
contigs = reader.contigs
paths = io_utils.maybe_generate_sharded_filenames(FLAGS.infile)
with tempfile.NamedTemporaryFile() as temp:
postprocess_variants_lib.process_single_sites_tfrecords(
contigs, paths, temp.name)
# Read one CallVariantsOutput record and extract the sample name from it.
# Note that this assumes that all CallVariantsOutput protos in the infile
# contain a single VariantCall within their constituent Variant proto, and
# that the call_set_name is identical in each of the records.
record = next(
io_utils.read_tfrecords(
paths[0],
proto=deepvariant_pb2.CallVariantsOutput,
max_records=1))
sample_name = _extract_single_sample_name(record)
independent_variants = _transform_call_variants_output_to_variants(
input_sorted_tfrecord_path=temp.name,
qual_filter=FLAGS.qual_filter,
multi_allelic_qual_filter=FLAGS.multi_allelic_qual_filter,
sample_name=sample_name)
variant_generator = haplotypes.maybe_resolve_conflicting_variants(
independent_variants)
write_variants_to_vcf(contigs=contigs,
variant_generator=variant_generator,
output_vcf_path=FLAGS.outfile,
sample_name=sample_name)
# Also write out the gVCF file if it was provided.
if FLAGS.nonvariant_site_tfrecord_path:
nonvariant_generator = io_utils.read_shard_sorted_tfrecords(
FLAGS.nonvariant_site_tfrecord_path,
key=_get_contig_based_variant_sort_keyfn(contigs),
proto=variants_pb2.Variant)
with genomics_io.make_vcf_reader(
FLAGS.outfile, use_index=False,
include_likelihoods=True) as variant_reader:
lessthanfn = _get_contig_based_lessthan(variant_reader.contigs)
gvcf_variants = (_transform_to_gvcf_record(variant)
for variant in variant_reader.iterate())
merged_variants = merge_variants_and_nonvariants(
gvcf_variants, nonvariant_generator, lessthanfn)
write_variants_to_vcf(contigs=contigs,
variant_generator=merged_variants,
output_vcf_path=FLAGS.gvcf_outfile,
sample_name=sample_name,
filters=FILTERS)
