def test_build_family_handlers(self):
args = Namespace(umt_distance_threshold=1, min_family_size_threshold=3)
handlers = build_family_handlers(args, samtools_test.MockAlignWriter(),
samtools_test.MockAlignWriter(),
self.mock_logger)
actual_handler_names = [x.__class__.__name__ for x in handlers]
expected_handler_names = [
'_FamilySizeStatHandler', '_MatchStatHandler',
'_WriteAnnotatedAlignsHandler', '_WriteConsensusHandler'
]
self.assertEqual(expected_handler_names, actual_handler_names)
def test_handle_excludeFilteredFamilies(self):
family_1 = _mock_tag_family(consensus=_mock_align_pair("readA"),
filter_value=None)
family_2 = _mock_tag_family(consensus=_mock_align_pair("readB"),
filter_value='foo')
families = [family_1, family_2]
writer = samtools_test.MockAlignWriter()
handler = _WriteConsensusHandler(writer)
for family in families:
handler.handle(family)
name_pairs = [(fam,
align.query_name) for fam, align in writer._write_calls]
self.assertEqual([(family_1, 'readA'), (family_1, 'readA')], name_pairs)
def test_handle_ordersAlignmentsByReadname(self):
pairA1 = _mock_align_pair("readA1")
pairA2 = _mock_align_pair("readA2")
pairA3 = _mock_align_pair("readA3")
pairA4 = _mock_align_pair("readA4")
family_A = _mock_tag_family(
align_pairs=set([pairA2, pairA1, pairA4, pairA3]))
families = [family_A]
writer = samtools_test.MockAlignWriter()
handler = _WriteAnnotatedAlignsHandler(writer)
for family in families:
handler.handle(family)
names = [align.query_name for _, align in writer._write_calls]
self.assertEqual([
'readA1', 'readA1', 'readA2', 'readA2', 'readA3', 'readA3',
'readA4', 'readA4'
], names)
def test_handle_writesAllAlignments(self):
pairA1 = _mock_align_pair("readA1")
pairA2 = _mock_align_pair("readA2", filter_value="foo")
pairB1 = _mock_align_pair("readB1")
pairB2 = _mock_align_pair("readB2", filter_value="bar")
family_A = _mock_tag_family(align_pairs=set([pairA1, pairA2]))
family_B = _mock_tag_family(align_pairs=set([pairB1, pairB2]))
families = [family_A, family_B]
writer = samtools_test.MockAlignWriter()
handler = _WriteAnnotatedAlignsHandler(writer)
for family in families:
handler.handle(family)
name_pairs = [(fam, align.query_name)
for fam, align in writer._write_calls]
self.assertEqual([(family_A, 'readA1'), (family_A, 'readA1'),
(family_A, 'readA2'), (family_A, 'readA2'),
(family_B, 'readB1'), (family_B, 'readB1'),
(family_B, 'readB2'), (family_B, 'readB2')],
name_pairs)
