def examples_to_variants(examples_path, max_records=None):
"""Yields Variant protos from the examples in examples_path.
This function reads in tf.Examples produced by DeepVariant from examples_path,
which may contain a sharded spec, sorts them, selects a representive example
when there are multiple versions representing different alt_alleles, and
yields the example_variant field from those examples.
Args:
examples_path: str. Path, or sharded spec, to labeled tf.Examples produced
by DeepVariant in training mode.
max_records: int or None. Maximum number of records to read, or None, to
read all of the records.
Yields:
nucleus.protos.Variant protos in coordinate-sorted order.
Raises:
ValueError: if we find a Variant in any example that doesn't have genotypes.
"""
examples = io_utils.read_tfrecords(examples_path, max_records=max_records)
variants = sorted(
(tf_utils.example_variant(example) for example in examples),
key=variant_utils.variant_range_tuple)
for _, group in itertools.groupby(variants,
variant_utils.variant_range_tuple):
variant = next(group)
if not variantcall_utils.has_genotypes(variant_utils.only_call(variant)):
raise ValueError((
'Variant {} does not have any genotypes. This tool only works with '
'variants that have been labeled.').format(
variant_utils.variant_key(variant)))
yield variant
def examples_to_variants(examples_path, max_records=None):
"""Yields Variant protos from the examples in examples_path.
This function reads in tf.Examples produced by DeepVariant from examples_path,
which may contain a sharded spec, sorts them, selects a representive example
when there are multiple versions representing different alt_alleles, and
yields the example_variant field from those examples.
Args:
examples_path: str. Path, or sharded spec, to labeled tf.Examples produced
by DeepVariant in training mode.
max_records: int or None. Maximum number of records to read, or None, to
read all of the records.
Yields:
nucleus.protos.Variant protos in coordinate-sorted order.
Raises:
ValueError: if we find a Variant in any example that doesn't have genotypes.
"""
examples = io_utils.read_tfrecords(examples_path, max_records=max_records)
variants = sorted(
(tf_utils.example_variant(example) for example in examples),
key=variant_utils.variant_range_tuple)
for _, group in itertools.groupby(variants,
variant_utils.variant_range_tuple):
variant = next(group)
if not variantcall_utils.has_genotypes(
variant_utils.only_call(variant)):
raise ValueError((
'Variant {} does not have any genotypes. This tool only works with '
'variants that have been labeled.').format(
variant_utils.variant_key(variant)))
yield variant
def test_vcf_caller_end2end_outputs(self):
# Confirming that the proposed VCF (input) has the same variants
# as the VCF output converted from the output of make_examples.
variants = list(
labeled_examples_to_vcf.examples_to_variants(
testdata.GOLDEN_VCF_CALLER_TRAINING_EXAMPLES))
with vcf.VcfReader(testdata.TRUTH_VARIANTS_VCF) as proposed_vcf_reader:
# This checks the keys (like chr20:10099832:A->G) are the same.
self.assertEqual([variant_utils.variant_key(v1) for v1 in variants], [
variant_utils.variant_key(v2) for v2 in proposed_vcf_reader.iterate()
])
with vcf.VcfReader(testdata.TRUTH_VARIANTS_VCF) as proposed_vcf_reader:
self.assertEqual(
[variant_utils.genotype_as_alleles(v1) for v1 in variants], [
variant_utils.genotype_as_alleles(
variant_utils.unphase_all_genotypes(v2))
for v2 in proposed_vcf_reader.iterate()
])
def main(argv):
del argv
contigs = fasta.RefFastaReader(FLAGS.ref).header.contigs
max_records = FLAGS.max_records if FLAGS.max_records >= 0 else None
variants_iter = examples_to_variants(FLAGS.examples, max_records=max_records)
if not FLAGS.sample_name:
sample_name, variants_iter = peek_sample_name(variants_iter)
else:
sample_name = FLAGS.sample_name
header = dv_vcf_constants.deepvariant_header(
contigs=contigs, sample_names=[sample_name])
with vcf.VcfWriter(FLAGS.output_vcf, header=header) as writer:
for variant in variants_iter:
variant.calls[0].call_set_name = sample_name
logging.log_every_n(logging.INFO, 'Converted %s', FLAGS.log_every,
variant_utils.variant_key(variant))
writer.write(variant)
def test_variant_key(self, variant, expected_key, sort_alleles=True):
self.assertEqual(
variant_utils.variant_key(variant, sort_alleles=sort_alleles),
expected_key)
def test_variant_key(self, variant, expected_key, sort_alleles=True):
self.assertEqual(
variant_utils.variant_key(variant, sort_alleles=sort_alleles),
expected_key)
def print_variants(name, variants):
logging.info('variants: %s [%d]', name, len(variants))
for v in variants:
logging.info(' %s gt=%s', variant_utils.variant_key(v),
_variant_genotypes([v])[0])
def _log_variants(name, variants):
"""Write basic information about variants to logging.info."""
logging.info('variants: %s [%d]', name, len(variants))
for v in variants:
logging.info(' %s gt=%s', variant_utils.variant_key(v),
_variant_genotypes([v])[0])
def print_variants(name, variants):
logging.info('variants: %s [%d]', name, len(variants))
for v in variants:
logging.info(' %s gt=%s', variant_utils.variant_key(v),
_variant_genotypes([v])[0])
