def test_exonic_five_prime_first_exon(self): b = Breakpoint('1', 150, orient=ORIENT.LEFT) breaks = pairing.predict_transcriptome_breakpoint( b, self.pre_transcript) self.assertEqual(1, len(breaks)) self.assertEqual(b, breaks[0])
def test_exonic_three_prime_last_exon(self): b = Breakpoint('1', 550, orient=ORIENT.RIGHT) breaks = pairing.predict_transcriptome_breakpoint( b, self.pre_transcript) self.assertEqual(1, len(breaks)) self.assertEqual(b, breaks[0])
def test_intronic_short_exon_right(self): b = Breakpoint(chr='1', start=1690, orient=ORIENT.RIGHT) print(self.genome_window(b)) self.assertEqual(Interval(1580, 3500), self.transcriptome_window(b))
def test_intronic_short_exon_left(self): b = Breakpoint(chr='1', start=2200, orient=ORIENT.LEFT) self.assertEqual(Interval(1440, 2310), self.transcriptome_window(b))
def test_exonic_three_prime(self, positive_transcript): b = Breakpoint('1', 350, orient=ORIENT.RIGHT) breaks = pairing.predict_transcriptome_breakpoint(b, positive_transcript) assert len(breaks) == 2 assert breaks[1].start == 501 assert breaks[0] == b
def test_intronic_long_intron(self): b = Breakpoint(chr='1', start=1800, orient=ORIENT.RIGHT) print(self.genome_window(b)) self.assertEqual(Interval(1490, 2360), self.transcriptome_window(b))
def test_before_start(self): b = Breakpoint(chr='1', start=100, orient=ORIENT.RIGHT) self.assertEqual(self.genome_window(b), self.transcriptome_window(b)) b = Breakpoint(chr='1', start=500, orient=ORIENT.RIGHT) self.assertEqual(self.genome_window(b), self.transcriptome_window(b))
def test_outside_transcript(self): b = Breakpoint('1', 100, orient=ORIENT.RIGHT) with self.assertRaises(AssertionError): pairing.predict_transcriptome_breakpoint(b, self.pre_transcript)
def test_exonic_five_prime_neg_last_exon(self, negative_transcript): b = Breakpoint('1', 550, orient=ORIENT.RIGHT) breaks = pairing.predict_transcriptome_breakpoint(b, negative_transcript) assert len(breaks) == 1 assert breaks[0] == b
def test_intronic_five_prime_neg(self, negative_transcript): b = Breakpoint('1', 250, orient=ORIENT.RIGHT) breaks = pairing.predict_transcriptome_breakpoint(b, negative_transcript) assert len(breaks) == 1 assert breaks[0].start == 301
def test_intronic_three_prime_neg(self, negative_transcript): b = Breakpoint('1', 450, orient=ORIENT.LEFT, strand=STRAND.NEG) breaks = pairing.predict_transcriptome_breakpoint(b, negative_transcript) assert len(breaks) == 1 assert breaks[0].start == 400
def test_outside_transcript(self, positive_transcript): b = Breakpoint('1', 100, orient=ORIENT.RIGHT) with pytest.raises(AssertionError): pairing.predict_transcriptome_breakpoint(b, positive_transcript)
def test_intronic_five_prime(self, positive_transcript): b = Breakpoint('1', 450, orient=ORIENT.LEFT) breaks = pairing.predict_transcriptome_breakpoint(b, positive_transcript) assert len(breaks) == 1 assert breaks[0].start == 400
def test_intronic_five_prime(self): b = Breakpoint('1', 450, orient=ORIENT.LEFT) breaks = pairing.predict_transcriptome_breakpoint( b, self.pre_transcript) self.assertEqual(1, len(breaks)) self.assertEqual(400, breaks[0].start)
def test_after_end(self): b = Breakpoint(chr='1', start=6000, orient=ORIENT.RIGHT) self.assertEqual(self.genome_window(b), self.transcriptome_window(b))
def test_intronic_three_prime(self): b = Breakpoint('1', 250, orient=ORIENT.RIGHT) breaks = pairing.predict_transcriptome_breakpoint( b, self.pre_transcript) self.assertEqual(1, len(breaks)) self.assertEqual(301, breaks[0].start)
def test_intronic_long_exon(self): b = Breakpoint(chr='1', start=2970, orient=ORIENT.RIGHT) self.assertEqual(self.genome_window(b), self.transcriptome_window(b))
def test_exonic_three_prime_neg(self): b = Breakpoint('1', 350, orient=ORIENT.LEFT, strand=STRAND.NEG) breaks = pairing.predict_transcriptome_breakpoint(b, self.n_ust) self.assertEqual(2, len(breaks)) self.assertEqual(200, breaks[0].start) self.assertEqual(b, breaks[1])
def test_exonic_five_prime_first_exon(self, positive_transcript): b = Breakpoint('1', 150, orient=ORIENT.LEFT) breaks = pairing.predict_transcriptome_breakpoint(b, positive_transcript) assert len(breaks) == 1 assert breaks[0] == b