def verify_examples(self, examples_filename, region, options,
verify_labels):
# Do some simple structural checks on the tf.Examples in the file.
expected_labels = [
'variant/encoded', 'locus', 'image/format', 'image/encoded',
'alt_allele_indices/encoded'
]
if verify_labels:
expected_labels += ['label', 'truth_variant/encoded']
examples = list(io_utils.read_tfrecords(examples_filename))
for example in examples:
for label_feature in expected_labels:
self.assertIn(label_feature, example.features.feature)
# pylint: disable=g-explicit-length-test
self.assertGreater(
len(tf_utils.example_alt_alleles_indices(example)), 0)
if verify_labels:
# Check that our variant and our truth_variant both have the same start.
self.assertEqual(
variantutils.variant_position(
tf_utils.example_variant(example)),
variantutils.variant_position(
tf_utils.example_truth_variant(example)))
# Check that the variants in the examples are good.
variants = [tf_utils.example_variant(x) for x in examples]
self.verify_variants(variants, region, options, is_gvcf=False)
return examples
def test_variant_position_and_range(self):
v1 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=10)
v2 = test_utils.make_variant(chrom='1',
alleles=['AGCT', 'C'],
start=10)
pos = ranges.make_range('1', 10, 11)
range_ = ranges.make_range('1', 10, 14)
self.assertEqual(pos, variantutils.variant_position(v1))
self.assertEqual(pos, variantutils.variant_position(v2))
self.assertEqual(pos, variantutils.variant_range(v1))
self.assertEqual(range_, variantutils.variant_range(v2))
def _find_matching_variant_in_reader(self, variant):
"""Finds a variant in vcf_reader compatible with variant, if one exists."""
def _usable_truth(truth_variant):
return (variant.start == truth_variant.start and
not variantutils.is_filtered(truth_variant))
region = variantutils.variant_position(variant)
matches = [m for m in self._vcf_reader.query(region) if _usable_truth(m)]
if not matches:
return None
elif len(matches) > 1:
logging.warning(
'Multiple matches detected, keeping first, for variant %s: %s',
variant, matches)
return matches[0]