def test_is_positive(self):
mock_alignment_file = MockAlignmentFile({1: "chr1"})
read = util.Read(MockAlignedSegment(is_reverse=False),
mock_alignment_file)
self.assertEquals(True, read.is_positive_strand)
read = util.Read(MockAlignedSegment(is_reverse=True),
mock_alignment_file)
self.assertEquals(False, read.is_positive_strand)
def test_set_tag(self):
mock_alignment_file = MockAlignmentFile({2: "chr2"})
mock_aligned_segment = MockAlignedSegment()
read = util.Read(mock_aligned_segment, mock_alignment_file)
read.set_tag("name", "value", "type")
self.assertEquals("name:type:value",
mock_aligned_segment._tags["name"])
def test_isPaired(self):
mock_alignment_file = MockAlignmentFile({1: "chr1"})
mock_aligned_segment = MockAlignedSegment(query_name="read1",
reference_id=1,
reference_start=100,
cigarstring="10M",
is_paired=True,
mate_is_unmapped=True,
mate_is_reverse=True,
is_proper_pair=True,
is_read1=True,
next_reference_id=1,
next_reference_start=200)
read = util.Read(mock_aligned_segment, mock_alignment_file)
read.is_paired = False
self.assertEquals(False, mock_aligned_segment.__dict__['is_paired'])
self.assertEquals(False,
mock_aligned_segment.__dict__['mate_is_unmapped'])
self.assertEquals(False,
mock_aligned_segment.__dict__['is_proper_pair'])
self.assertEquals(False, mock_aligned_segment.__dict__['is_read1'])
self.assertEquals(-1,
mock_aligned_segment.__dict__['next_reference_id'])
self.assertEquals(
0, mock_aligned_segment.__dict__['next_reference_start'])
def test_mate_key_noneWhenNoMate(self):
mock_alignment_file = MockAlignmentFile({2: "chr2"})
#pylint: disable=attribute-defined-outside-init
mock_aligned_segment = MockAlignedSegment(query_name="read1",
is_paired=True,
mate_is_unmapped=False,
mate_is_reverse=True,
next_reference_id=2,
next_reference_start=200)
mock_aligned_segment.is_paired = False
read = util.Read(mock_aligned_segment, mock_alignment_file)
self.assertEquals(None, read.mate_key)
mock_aligned_segment.is_paired = True
mock_aligned_segment.mate_is_unmapped = True
read = util.Read(mock_aligned_segment, mock_alignment_file)
self.assertEquals(None, read.mate_key)
def test_key(self):
mock_alignment_file = MockAlignmentFile({1: "chr1"})
mock_aligned_segment = MockAlignedSegment(query_name="readA",
reference_id=1,
reference_start=100,
is_reverse=False,
is_read1=True)
read = util.Read(mock_aligned_segment, mock_alignment_file)
expected_key = ("readA", True, "chr1", 100, True)
self.assertEquals(expected_key, read.key)
def test_mate_key(self):
mock_alignment_file = MockAlignmentFile({2: "chr2"})
mock_aligned_segment = MockAlignedSegment(query_name="readA",
is_paired=True,
mate_is_unmapped=False,
mate_is_reverse=True,
next_reference_id=2,
next_reference_start=200,
is_read1=True)
read = util.Read(mock_aligned_segment, mock_alignment_file)
expected_key = ("readA", False, "chr2", 200, False)
self.assertEquals(expected_key, read.mate_key)
def test_init(self):
mock_alignment_file = MockAlignmentFile({1: "chr1"})
mock_aligned_segment = MockAlignedSegment(query_name="readA",
reference_id=1,
reference_start=100,
reference_end=110,
cigarstring="10M",
is_paired=True)
read = util.Read(mock_aligned_segment, mock_alignment_file)
self.assertEquals("readA", read.query_name)
self.assertEquals("chr1", read.reference_name)
self.assertEquals(100, read.reference_start)
self.assertEquals(110, read.reference_end)
self.assertEquals("10M", read.cigarstring)
self.assertEquals(True, read.is_paired)
def test_mutatorsPassThroughToAlignedSegment(self):
mock_alignment_file = MockAlignmentFile({1: "chr1"})
mock_aligned_segment = MockAlignedSegment(query_name="read1",
reference_id=1,
reference_start=100,
cigarstring="10M",
next_reference_start=150)
read = util.Read(mock_aligned_segment, mock_alignment_file)
read.reference_start = 142
read.cigarstring = "10S"
read.next_reference_start = 200
self.assertEquals(142,
mock_aligned_segment.__dict__['reference_start'])
self.assertEquals("10S", mock_aligned_segment.__dict__['cigarstring'])
self.assertEquals(
200, mock_aligned_segment.__dict__['next_reference_start'])