def test_filter_builder_multiple(self):
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=True),
is_unmapped=False,
is_cigar_valid=False)
self.assertEquals(["UNMATCHED_PRIMER_PAIR", "INVALID_CIGAR"],
clipper._filter_builder(transform))
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=True),
is_unmapped=True,
is_cigar_valid=False)
self.assertEquals(["UNMAPPED_ALIGNMENT"],
clipper._filter_builder(transform))
def test_handle(self):
read1 = MockRead(is_positive_strand=True)
read2 = MockRead(is_positive_strand=True)
primer_pair = MockPrimerPair(target_id="target_1",
chrom="chr1",
sense_start=242)
new_reference_start = 102
new_cigar_string = "2S8M"
transformation = MicroMock(primer_pair=primer_pair,
reference_start=new_reference_start,
cigar=new_cigar_string)
mate_transformation = None
mock_primer_stats = MockPrimerStats()
mock_primer_stats_dumper = MockPrimerStatsDumper()
handler = readhandler.StatsHandler(mock_primer_stats,
mock_primer_stats_dumper)
handler.handle(read1, transformation, mate_transformation)
handler.handle(read2, transformation, mate_transformation)
expected_calls = [(read1, primer_pair), (read2, primer_pair)]
self.assertEquals(expected_calls,
mock_primer_stats._add_read_primer_calls)
handler.end()
self.assertEquals([mock_primer_stats],
mock_primer_stats_dumper._dump_calls)
def test_handle_addsFiltersWhenPresent(self):
#pylint: disable=no-member
read = MockRead(reference_start=100,
reference_end=110,
cigarstring="10M")
primer_pair_target = "target_1"
primer_pair = MockPrimerPair(target_id=primer_pair_target)
transformation = MicroMock(primer_pair=primer_pair,
filters=("filter1", "filter2"))
mate_transformation = None
handler = readhandler.AddTagsReadHandler()
handler.handle(read, transformation, mate_transformation)
self.assertEquals("X4:Z:" + "filter1,filter2", read._tags["X4"])
def test_handle(self):
#pylint: disable=no-member
original_reference_start = 100
original_reference_end = 110
original_cigar_string = "10M"
read = MockRead(reference_start=original_reference_start,
reference_end=original_reference_end,
cigarstring=original_cigar_string)
primer_pair_target = "target_1"
primer_pair = MockPrimerPair(target_id=primer_pair_target)
transformation = MicroMock(primer_pair=primer_pair, filters=())
mate_transformation = None
handler = readhandler.AddTagsReadHandler()
handler.handle(read, transformation, mate_transformation)
self.assertEquals("X0:Z:" + primer_pair_target, read._tags["X0"])
self.assertEquals("X1:Z:" + original_cigar_string, read._tags["X1"])
self.assertEquals("X2:i:" + str(original_reference_start),
read._tags["X2"])
self.assertEquals("X3:i:" + str(original_reference_end),
read._tags["X3"])
def test_filter_builder_invalidCigar(self):
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=False),
is_unmapped=False,
is_cigar_valid=False)
self.assertEquals(["INVALID_CIGAR"],
clipper._filter_builder(transform))
def test_filter_builder_unmappedAlignment(self):
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=False),
is_unmapped=True,
is_cigar_valid=True)
self.assertEquals(["UNMAPPED_ALIGNMENT"],
clipper._filter_builder(transform))
def test_filter_builder_unmatchedPrimerPair(self):
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=True),
is_unmapped=False,
is_cigar_valid=True)
self.assertEquals(["UNMATCHED_PRIMER_PAIR"],
clipper._filter_builder(transform))
def test_filter_builder_noFilters(self):
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=False),
is_unmapped=False,
is_cigar_valid=True)
self.assertEquals([], clipper._filter_builder(transform))