Python Contig.add_mapped_sequence Examples

Example #1

File: test_align.py Project: bcgsc/mavis

    def test_break_left_deletion(self):
        contig = Contig(' ' * 60, None)
        contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=10))
        contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=20))
        contig.add_mapped_sequence(MockObject(reference_start=50, reference_end=60))

        b = Breakpoint('10', 1030, 1030, orient=ORIENT.LEFT)
        read = MockRead(
            cigar=_cigar.convert_string_to_cigar('35M10D5I20M'),
            reference_start=999,
            reference_name='10',
        )
        align.SplitAlignment.breakpoint_contig_remapped_depth(b, contig, read)

Example #2

class TestBreakpointContigRemappedDepth(unittest.TestCase):
    def setUp(self):
        self.contig = Contig(' ' * 60, None)
        self.contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=10))
        self.contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=20))
        self.contig.add_mapped_sequence(MockObject(reference_start=50, reference_end=60))

    def test_break_left_deletion(self):
        b = Breakpoint('10', 1030, 1030, orient=ORIENT.LEFT)
        read = MockRead(
            cigar=_cigar.convert_string_to_cigar('35M10D5I20M'),
            reference_start=999,
            reference_name='10'
        )
        align.SplitAlignment.breakpoint_contig_remapped_depth(b, self.contig, read)