def label_variant(self, example, variant):
"""Adds the truth variant and label for variant to example.
This function uses VariantLabeler to find a match for variant and writes
in the correspond truth variant and derived label to our example proto.
Args:
example: A tf.Example proto. We will write truth_variant and label into
this proto.
variant: A learning.genomics.v1.Variant proto.
This is the variant we'll use
to call our VariantLabeler.match to get our truth variant.
Returns:
True if the variant was in the confident region (meaning that it could be
given a label) and False otherwise.
"""
is_confident, truth_variant = self.labeler.match(variant)
if not is_confident:
return False
alt_alleles = tf_utils.example_alt_alleles(example, variant=variant)
if variantutils.is_ref(variant):
label = 0
else:
label = self.labeler.match_to_alt_count(variant, truth_variant,
alt_alleles)
tf_utils.example_set_label(example, label)
tf_utils.example_set_truth_variant(example, truth_variant)
return True
def add_label_to_example(self, example, label):
"""Adds label information about the assigned label to our example.
Args:
example: A tf.Example proto. We will write truth_variant and label into
this proto.
label: A variant_labeler.Label object containing the labeling information
to add to our example.
Returns:
The example proto with label fields added.
Raises:
ValueError: if label isn't confident.
"""
if not label.is_confident:
raise ValueError('Cannot add a non-confident label to an example',
example, label)
alt_alleles_indices = tf_utils.example_alt_alleles_indices(example)
# Set the genotype of the candidate variant to the labeled value.
candidate = label.variant
_set_variant_genotype(candidate, label.genotype)
tf_utils.example_set_variant(example, candidate)
# Set the label of the example to the # alts given our alt_alleles_indices.
tf_utils.example_set_label(example,
label.label_for_alt_alleles(alt_alleles_indices))
return example
def testExampleSetLabel(self):
example = tf_utils.make_example(self.variant, self.alts, self.encoded_image,
self.default_shape, self.default_format)
self.assertIsNotAFeature('label', example)
for label in [0, 1, 2]:
tf_utils.example_set_label(example, label)
self.assertEqual(label, tf_utils.example_label(example))