def test_create_pileup_examples(self):
self.processor.pic = mock.Mock()
self.add_mock('_encode_tensor',
side_effect=[
('tensor1', self.default_shape, self.default_format),
('tensor2', self.default_shape, self.default_format)
])
dv_call = mock.Mock()
dv_call.variant = test_utils.make_variant(start=10,
alleles=['A', 'C', 'G'])
ex = mock.Mock()
alt1, alt2 = ['C'], ['G']
self.processor.pic.create_pileup_images.return_value = [
(alt1, 'tensor1'), (alt2, 'tensor2')
]
actual = self.processor.create_pileup_examples(dv_call)
self.processor.pic.create_pileup_images.assert_called_once_with(
dv_call)
self.assertEquals(len(actual), 2)
for ex, (alt, img) in zip(actual, [(alt1, 'tensor1'),
(alt2, 'tensor2')]):
self.assertEqual(tf_utils.example_alt_alleles(ex), alt)
self.assertEqual(tf_utils.example_variant(ex), dv_call.variant)
self.assertEqual(tf_utils.example_encoded_image(ex), img)
self.assertEqual(tf_utils.example_image_shape(ex),
self.default_shape)
self.assertEqual(tf_utils.example_image_format(ex),
self.default_format)
def testMakeExample(self):
example = tf_utils.make_example(self.variant, self.alts, self.encoded_image,
self.default_shape, self.default_format)
self.assertEqual(self.encoded_image,
tf_utils.example_encoded_image(example))
self.assertEqual(
'raw', example.features.feature['image/format'].bytes_list.value[0])
self.assertEqual(self.variant, tf_utils.example_variant(example))
self.assertEqual('1:11-11', tf_utils.example_locus(example))
self.assertEqual([0], tf_utils.example_alt_alleles_indices(example))
self.assertEqual('1:11:C->A', tf_utils.example_key(example))
def test_create_pileup_examples(self):
self.processor.pic = mock.Mock()
self.add_mock(
'_encode_tensor',
side_effect=[('tensor1', self.default_shape, self.default_format),
('tensor2', self.default_shape, self.default_format)])
dv_call = mock.Mock()
dv_call.variant = test_utils.make_variant(start=10, alleles=['A', 'C', 'G'])
ex = mock.Mock()
alt1, alt2 = ['C'], ['G']
self.processor.pic.create_pileup_images.return_value = [(alt1, 'tensor1'),
(alt2, 'tensor2')]
actual = self.processor.create_pileup_examples(dv_call)
self.processor.pic.create_pileup_images.assert_called_once_with(dv_call)
self.assertEquals(len(actual), 2)
for ex, (alt, img) in zip(actual, [(alt1, 'tensor1'), (alt2, 'tensor2')]):
self.assertEqual(tf_utils.example_alt_alleles(ex), alt)
self.assertEqual(tf_utils.example_variant(ex), dv_call.variant)
self.assertEqual(tf_utils.example_encoded_image(ex), img)
self.assertEqual(tf_utils.example_image_shape(ex), self.default_shape)
self.assertEqual(tf_utils.example_image_format(ex), self.default_format)
def test_create_pileup_examples(self):
self.processor.pic = mock.Mock()
self.processor.pic.get_reads.return_value = []
self.add_mock('_encode_tensor',
side_effect=[(six.b('tensor1'), self.default_shape,
self.default_format),
(six.b('tensor2'), self.default_shape,
self.default_format)])
dv_call = mock.Mock()
dv_call.variant = test_utils.make_variant(start=10,
alleles=['A', 'C', 'G'])
ex = mock.Mock()
alt1, alt2 = ['C'], ['G']
self.processor.pic.create_pileup_images.return_value = [
(alt1, six.b('tensor1')), (alt2, six.b('tensor2'))
]
actual = self.processor.create_pileup_examples(dv_call)
self.processor.pic.create_pileup_images.assert_called_once_with(
dv_call=dv_call,
reads_for_samples=[[]],
haplotype_alignments_for_samples=None,
haplotype_sequences=None,
sample_order=None)
self.assertLen(actual, 2)
for ex, (alt, img) in zip(actual, [(alt1, six.b('tensor1')),
(alt2, six.b('tensor2'))]):
self.assertEqual(tf_utils.example_alt_alleles(ex), alt)
self.assertEqual(tf_utils.example_variant(ex), dv_call.variant)
self.assertEqual(tf_utils.example_encoded_image(ex), img)
self.assertEqual(tf_utils.example_image_shape(ex),
self.default_shape)
self.assertEqual(tf_utils.example_image_format(ex),
six.b(self.default_format))