def test_process_with_realigner(self):
self.processor.options.mode = deepvariant_pb2.DeepVariantOptions.CALLING
self.processor.options.realigner_options.CopyFrom(
realigner_pb2.RealignerOptions())
self.processor.realigner = mock.Mock()
self.processor.realigner.realign_reads.return_value = [], []
self.processor.sam_reader = mock.Mock()
self.processor.sam_reader.query.return_value = []
self.processor.in_memory_sam_reader = mock.Mock()
c1, c2 = mock.Mock(), mock.Mock()
e1, e2, e3 = mock.Mock(), mock.Mock(), mock.Mock()
self.add_mock('candidates_in_region', retval=([c1, c2], []))
mock_cpe = self.add_mock('create_pileup_examples',
side_effect=[[e1], [e2, e3]])
mock_lv = self.add_mock('label_variant')
self.assertEqual(([c1, c2], [e1, e2, e3], []),
self.processor.process(self.region))
self.processor.sam_reader.query.assert_called_once_with(self.region)
self.processor.realigner.realign_reads.assert_called_once_with(
[], self.region)
self.processor.in_memory_sam_reader.replace_reads.assert_called_once_with(
[])
self.assertEqual([mock.call(c1), mock.call(c2)],
mock_cpe.call_args_list)
test_utils.assert_not_called_workaround(mock_lv)
def test_process_keeps_ordering_of_candidates_and_examples(self, mode):
self.processor.options.mode = mode
r1, r2 = mock.Mock(), mock.Mock()
c1, c2 = mock.Mock(), mock.Mock()
e1, e2, e3 = mock.Mock(), mock.Mock(), mock.Mock()
self.processor.in_memory_sam_reader = mock.Mock()
self.add_mock('region_reads', retval=[r1, r2])
self.add_mock('candidates_in_region', retval=([c1, c2], []))
mock_cpe = self.add_mock('create_pileup_examples',
side_effect=[[e1], [e2, e3]])
mock_lv = self.add_mock('label_variant')
self.assertEqual(([c1, c2], [e1, e2, e3], []),
self.processor.process(self.region))
self.processor.in_memory_sam_reader.replace_reads.assert_called_once_with(
[r1, r2])
# We don't try to label variants when in calling mode.
self.assertEqual([mock.call(c1), mock.call(c2)],
mock_cpe.call_args_list)
if mode == deepvariant_pb2.DeepVariantOptions.CALLING:
# In calling mode, we never try to label.
test_utils.assert_not_called_workaround(mock_lv)
else:
self.assertEqual([
mock.call(e1, c1.variant),
mock.call(e2, c2.variant),
mock.call(e3, c2.variant)
], mock_lv.call_args_list)
def test_process_calls_with_candidates(self, mode):
self.processor.options.mode = mode
self.processor.in_memory_sam_reader = mock.Mock()
mock_read = mock.MagicMock()
mock_candidate = mock.MagicMock()
mock_example = mock.MagicMock()
mock_rr = self.add_mock('region_reads', retval=[mock_read])
mock_cir = self.add_mock('candidates_in_region',
retval=([mock_candidate], []))
mock_cpe = self.add_mock('create_pileup_examples',
retval=[mock_example])
mock_lv = self.add_mock('label_variant')
self.assertEqual(([mock_candidate], [mock_example], []),
self.processor.process(self.region))
mock_rr.assert_called_once_with(self.region)
self.processor.in_memory_sam_reader.replace_reads.assert_called_once_with(
[mock_read])
mock_cir.assert_called_once_with(self.region)
mock_cpe.assert_called_once_with(mock_candidate)
if mode == deepvariant_pb2.DeepVariantOptions.CALLING:
# In calling mode, we never try to label.
test_utils.assert_not_called_workaround(mock_lv)
else:
mock_lv.assert_called_once_with(mock_example,
mock_candidate.variant)
def test_model_init_function(self, path, expected):
model = mock.Mock(spec=modeling.DeepVariantModel)
model.initialize_from_checkpoint.return_value = MOCK_SENTINEL_RETURN_VALUE
self.assertEqual(expected, model_train.model_init_function(model, 3, path))
if expected:
model.initialize_from_checkpoint.assert_called_once_with(
path, 3, is_training=True)
else:
test_utils.assert_not_called_workaround(model.initialize_from_checkpoint)
def test_image_no_reads(self):
# This image is created just from reference and no reads. Checks that the
# function is listening to all of our image creation parameters (e.g.,
# reference_band_height, width, height, etc) and is filling the image with
# empty rows when it runs out of reads.
image = self.pic.build_pileup(self.dv_call, self.ref, [],
{self.alt_allele})
self.mock_enc_ref.assert_called_once_with(self.ref)
test_utils.assert_not_called_workaround(self.mock_enc_read)
self.assertImageMatches(image, 'ref', 'ref', 'empty', 'empty')
def test_candidates_in_region_no_reads(self):
self.processor.in_memory_sam_reader = mock.Mock()
self.processor.in_memory_sam_reader.query.return_value = []
mock_ac = self.add_mock('_make_allele_counter_for_region')
self.assertEqual(([], []), self.processor.candidates_in_region(self.region))
self.processor.in_memory_sam_reader.query.assert_called_once_with(
self.region)
# A region with no reads should return out without making an AlleleCounter.
test_utils.assert_not_called_workaround(mock_ac)
def test_on_demand_initialization_not_called_if_initialized(self):
self.processor.initialized = True
self.assertTrue(self.processor.initialized)
self.processor.in_memory_sam_reader = mock.Mock()
mock_rr = self.add_mock('region_reads', retval=[])
mock_cir = self.add_mock('candidates_in_region', retval=([], []))
self.processor.process(self.region)
test_utils.assert_not_called_workaround(self.mock_init)
mock_rr.assert_called_once_with(self.region)
self.processor.in_memory_sam_reader.replace_reads.assert_called_once_with(
[])
mock_cir.assert_called_once_with(self.region)
def test_process_calls_no_candidates(self):
self.processor.in_memory_sam_reader = mock.Mock()
mock_rr = self.add_mock('region_reads', retval=[])
mock_cir = self.add_mock('candidates_in_region', retval=([], []))
mock_cpe = self.add_mock('create_pileup_examples', retval=[])
mock_lv = self.add_mock('label_variant')
self.assertEqual(([], [], []), self.processor.process(self.region))
mock_rr.assert_called_once_with(self.region)
self.processor.in_memory_sam_reader.replace_reads.assert_called_once_with(
[])
mock_cir.assert_called_once_with(self.region)
test_utils.assert_not_called_workaround(mock_cpe)
test_utils.assert_not_called_workaround(mock_lv)