def test_handle_logsExclusions(self):
#pylint: disable=no-member
read = MockRead()
mate_transform = MicroMock(filters=())
mock_log = MockLog()
handler = ExcludeNonMatchedReadHandler(log_method=mock_log.log)
try:
handler.handle(read, MicroMock(filters=("filterA")),
mate_transform)
except StopIteration:
pass
try:
handler.handle(read, MicroMock(filters=("filterA")),
mate_transform)
except StopIteration:
pass
try:
handler.handle(read, MicroMock(filters=("filterB")),
mate_transform)
except StopIteration:
pass
self.assertEquals(2, len(handler._all_exclusions))
self.assertEquals(2, handler._all_exclusions["filterA"])
self.assertEquals(1, handler._all_exclusions["filterB"])
handler.end()
self.assertEquals(2, len(mock_log._log_calls))
def test_handle_noExceptionIfNoFilters(self):
read = MockRead()
transformation = MicroMock(filters=())
mate_transformation = MicroMock(filters=())
mock_log = MockLog()
handler = ExcludeNonMatchedReadHandler(log_method=mock_log.log)
handler.handle(read, transformation, mate_transformation)
self.assertEquals(True, True)
def test_handle_raisesIfTransformHasFilter(self):
#pylint: disable=no-member
read = MockRead()
transformation = MicroMock(filters=("filterA"))
mate_transformation = MicroMock(filters=())
mock_log = MockLog()
handler = ExcludeNonMatchedReadHandler(log_method=mock_log.log)
self.assertRaises(StopIteration, handler.handle, read, transformation,
mate_transformation)
def test_handle_unpairsReadIfMateHasFilter(self):
#pylint: disable=no-member
read = MockRead()
transformation = MicroMock(filters=())
mate_transformation = MicroMock(filters=("filterA"))
mock_log = MockLog()
handler = readhandler.ExcludeNonMatchedReadHandler(log_method=mock_log)
handler.handle(read, transformation, mate_transformation)
self.assertEquals(False, read.is_paired)
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_cigar_factory_nullCigar(self):
mock_read = MicroMock(reference_start=42, cigarstring="*")
c = cigar.cigar_factory(mock_read)
self.assertIsInstance(c, cigar.NullCigarUtil)
self.assertEquals(42, c.reference_start)
self.assertEquals("*", c.cigar)
mock_read = MicroMock(reference_start=42, cigarstring="")
c = cigar.cigar_factory(mock_read)
self.assertIsInstance(c, cigar.NullCigarUtil)
self.assertEquals(42, c.reference_start)
self.assertEquals("*", c.cigar)
def test_peak_memory(self):
resource_getrusage_orig = resource.getrusage
sys_platform_orig = sys.platform
try:
sys.platform = "darwin"
resource.getrusage = lambda x: MicroMock(ru_maxrss=4200000)
self.assertEquals(4, clipper._peak_memory())
sys.platform = "linux"
resource.getrusage = lambda x: MicroMock(ru_maxrss=4200)
self.assertEquals(4, clipper._peak_memory())
finally:
resource.getrusage = resource_getrusage_orig
sys.platform = sys_platform_orig
def test_handle_doesNotResetNextStartIfMateUnmapped(self):
#pylint: disable=no-member
reference_start = 111
original_next_reference_start = 333
read = MockRead(reference_start=reference_start,
cigarstring="10M",
next_reference_start=original_next_reference_start,
is_paired=True)
new_reference_start = 222
transformation = MicroMock(reference_start=new_reference_start,
cigar="10M")
mate_transformation = MicroMock(is_unmapped=True, reference_start=333)
handler = readhandler.TransformReadHandler()
handler.handle(read, transformation, mate_transformation)
self.assertEquals(original_next_reference_start,
read.next_reference_start)
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(self):
#pylint: disable=no-member
read = MockRead(reference_start=100,
cigarstring="10M",
next_reference_start=150,
is_paired=True)
new_reference_start = 102
new_cigar_string = "2S8M"
new_next_ref_start = 200
transformation = MicroMock(primer_pair=None,
reference_start=new_reference_start,
cigar=new_cigar_string)
mate_transformation = MicroMock(primer_pair=None,
reference_start=new_next_ref_start,
ciagr="",
is_unmapped=False)
handler = readhandler.TransformReadHandler()
handler.handle(read, transformation, mate_transformation)
self.assertEquals(new_reference_start, read.reference_start)
self.assertEquals(new_cigar_string, read.cigarstring)
self.assertEquals(new_next_ref_start, read.next_reference_start)
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_ignoresMateIfUnpaired(self):
#pylint: disable=no-member
reference_start = 150
read = MockRead(reference_start=100,
cigarstring="10M",
next_reference_start=reference_start,
is_paired=False)
new_reference_start = 102
new_cigar_string = "2S8M"
transformation = MicroMock(primer_pair=None,
reference_start=new_reference_start,
cigar=new_cigar_string)
mate_transformation = None
handler = readhandler.TransformReadHandler()
handler.handle(read, transformation, mate_transformation)
self.assertEquals(reference_start, read.next_reference_start)
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_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_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_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_noFilters(self):
transform = MicroMock(primer_pair=MockPrimerPair(is_unmatched=False),
is_unmapped=False,
is_cigar_valid=True)
self.assertEquals([], clipper._filter_builder(transform))