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
