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)