def test_before_start(self, trans_window_setup):
b = Breakpoint(chr='1', start=100, orient=ORIENT.RIGHT)
assert transcriptome_window(
trans_window_setup.trans_evidence, b
) == GenomeEvidence.generate_window(trans_window_setup.genome_evidence, b)
b = Breakpoint(chr='1', start=500, orient=ORIENT.RIGHT)
assert transcriptome_window(
trans_window_setup.trans_evidence, b
) == GenomeEvidence.generate_window(trans_window_setup.genome_evidence, b)
def test_orient_right(self):
bpp = Breakpoint(chr='1', start=1000, end=1000, orient=ORIENT.RIGHT)
window = GenomeEvidence.generate_window(
MockObject(read_length=100,
call_error=11,
max_expected_fragment_size=550), bpp)
self.assertEqual(890, window.start)
self.assertEqual(1560, window.end)
self.assertEqual(671, len(window))
def test_orient_right(self):
bpp = Breakpoint(chr='1', start=1000, end=1000, orient=ORIENT.RIGHT)
window = GenomeEvidence.generate_window(
MockObject(
read_length=100,
max_expected_fragment_size=550,
config={**DEFAULTS, 'validate.call_error': 11},
),
bpp,
)
assert window.start == 890
assert window.end == 1560
assert len(window) == 671
def test_intronic_long_exon(self, trans_window_setup):
b = Breakpoint(chr='1', start=2970, orient=ORIENT.RIGHT)
assert transcriptome_window(
trans_window_setup.trans_evidence, b
) == GenomeEvidence.generate_window(trans_window_setup.genome_evidence, b)
def genome_window(self, breakpoint):
return GenomeEvidence.generate_window(self.genome_evidence, breakpoint)