def test_net_zero(self):
transcript = PreTranscript([(1001, 1100), (1301, 1400), (1701, 1800)], strand=STRAND.POS)
for patt in transcript.generate_splicing_patterns():
transcript.transcripts.append(Transcript(transcript, patt))
trans_evidence = MockObject(
annotations={},
read_length=100,
max_expected_fragment_size=550,
call_error=11,
overlapping_transcripts={transcript},
)
setattr(
trans_evidence,
'_select_transcripts',
lambda *pos: trans_evidence.overlapping_transcripts,
)
setattr(
trans_evidence,
'distance',
partial(TranscriptomeEvidence.distance, trans_evidence),
)
bpp = BreakpointPair(
Breakpoint('1', 1099, orient=ORIENT.LEFT),
Breakpoint('1', 1302, orient=ORIENT.RIGHT),
untemplated_seq='TT',
)
dist = partial(TranscriptomeEvidence.distance, trans_evidence)
assert bpp.net_size() == Interval(-200)
assert bpp.net_size(dist) == Interval(0)
def test_net_zero(self):
bpp = BreakpointPair(Breakpoint('1', 1099, orient=ORIENT.LEFT),
Breakpoint('1', 1302, orient=ORIENT.RIGHT),
untemplated_seq='TT')
dist = partial(TranscriptomeEvidence.distance, self.trans_evidence)
self.assertEqual(Interval(-200), bpp.net_size())
self.assertEqual(Interval(0), bpp.net_size(dist))
def test_insertion(self):
bpp = BreakpointPair(Breakpoint('1', 11, orient=ORIENT.RIGHT),
Breakpoint('1', 10, orient=ORIENT.LEFT),
untemplated_seq='T')
self.assertEqual(Interval(1), bpp.net_size())
bpp = BreakpointPair(Breakpoint('1', 11, orient=ORIENT.RIGHT),
Breakpoint('1', 10, orient=ORIENT.LEFT),
untemplated_seq='TT')
self.assertEqual(Interval(2), bpp.net_size())
def test_deletion_in_exon(self):
bpp = BreakpointPair(Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='')
self.assertEqual(Interval(-8), bpp.net_size(self.egfr_distance))
bpp = BreakpointPair(Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='GTAC')
self.assertEqual(Interval(-4), bpp.net_size(self.egfr_distance))
def test_deletion_across_intron(self):
# 55240539_55240621 55323947_55324313
bpp = BreakpointPair(Breakpoint('7', 55240610, orient=ORIENT.LEFT),
Breakpoint('7', 55323950, orient=ORIENT.RIGHT),
untemplated_seq='GTAC')
self.assertEqual(Interval(-10), bpp.net_size(self.egfr_distance))
# 55210998_55211181 55218987_55219055
bpp = BreakpointPair(Breakpoint('7', 55211180, orient=ORIENT.LEFT),
Breakpoint('7', 55218990, orient=ORIENT.RIGHT),
untemplated_seq='')
self.assertEqual(Interval(-4 + -135, -4),
bpp.net_size(self.egfr_distance))
def test_deletion_in_exon(self, egfr_evidence):
bpp = BreakpointPair(
Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-8)
bpp = BreakpointPair(
Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='GTAC',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-4)
def test_deletion(self):
bpp = BreakpointPair(
Breakpoint('1', 10, orient=ORIENT.LEFT),
Breakpoint('1', 15, orient=ORIENT.RIGHT),
untemplated_seq='',
)
assert bpp.net_size() == Interval(-4)
def test_indel(self):
bpp = BreakpointPair(
Breakpoint('1', 13, orient=ORIENT.RIGHT),
Breakpoint('1', 10, orient=ORIENT.LEFT),
untemplated_seq='TTT',
)
assert bpp.net_size() == Interval(1)
def test_inversion_insertion(self):
bpp = BreakpointPair(
Breakpoint('1', 10, orient=ORIENT.LEFT),
Breakpoint('1', 15, orient=ORIENT.LEFT),
untemplated_seq='TT',
)
assert bpp.net_size() == Interval(2)
def test_inversion(self):
bpp = BreakpointPair(
Breakpoint('1', 10, orient=ORIENT.LEFT),
Breakpoint('1', 15, orient=ORIENT.LEFT),
untemplated_seq='',
)
self.assertEqual(Interval(0), bpp.net_size())
def test_duplication_with_insertion(self):
bpp = BreakpointPair(
Breakpoint('1', 10, orient=ORIENT.RIGHT),
Breakpoint('1', 15, orient=ORIENT.LEFT),
untemplated_seq='TTT',
)
self.assertEqual(Interval(9), bpp.net_size())
def test_large_indel(self):
bpp = BreakpointPair(
Breakpoint('1', 10, orient=ORIENT.LEFT),
Breakpoint('1', 101, orient=ORIENT.RIGHT),
untemplated_seq='TTT',
)
self.assertEqual(Interval(-87), bpp.net_size())
def test_deletion_across_intron(self, egfr_evidence):
# 55240539_55240621 55323947_55324313
bpp = BreakpointPair(
Breakpoint('7', 55240610, orient=ORIENT.LEFT),
Breakpoint('7', 55323950, orient=ORIENT.RIGHT),
untemplated_seq='GTAC',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-10)
# 55210998_55211181 55218987_55219055
bpp = BreakpointPair(
Breakpoint('7', 55211180, orient=ORIENT.LEFT),
Breakpoint('7', 55218990, orient=ORIENT.RIGHT),
untemplated_seq='',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-4 + -135, -4)
def test_insertion_at_exon_start_mixed(self):
# EXON 15: 55232973-55233130
# EXON 16: 55238868-55238906
# EXON 17: 55240676-55240817
bpp = BreakpointPair(Breakpoint('7', 55238867, orient=ORIENT.LEFT),
Breakpoint('7', 55238868, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG')
self.assertEqual(Interval(6), bpp.net_size(self.egfr_distance))
def test_indel_in_intron(self):
# 55238868_55238906
bpp = BreakpointPair(
Breakpoint('7', 5523700, orient=ORIENT.LEFT),
Breakpoint('7', 5523751, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
self.assertEqual(Interval(-44), bpp.net_size(self.egfr_distance))
def test_insertion_at_exon_end_mixed(self):
# 55238868_55238906
bpp = BreakpointPair(
Breakpoint('7', 55238905, orient=ORIENT.LEFT),
Breakpoint('7', 55238906, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
self.assertEqual(Interval(6), bpp.net_size(self.egfr_distance))
def test_insertion_at_exon_start(self, egfr_evidence):
# 55238868_55238906
bpp = BreakpointPair(
Breakpoint('7', 55233130, orient=ORIENT.LEFT),
Breakpoint('7', 55238868, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(6)
def test_indel_in_intron(self, egfr_evidence):
# 55238868_55238906
bpp = BreakpointPair(
Breakpoint('7', 5523700, orient=ORIENT.LEFT),
Breakpoint('7', 5523751, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-44)
def test_insertion_at_exon_start_mixed(self, egfr_evidence):
# EXON 15: 55232973-55233130
# EXON 16: 55238868-55238906
# EXON 17: 55240676-55240817
bpp = BreakpointPair(
Breakpoint('7', 55238867, orient=ORIENT.LEFT),
Breakpoint('7', 55238868, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(6)
def test_deletion_with_useq(self):
bpp = BreakpointPair(Breakpoint('1', 6964, orient='L'),
Breakpoint('1', 7040, orient='R'),
opposing=False,
untemplated_seq='CCCT')
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(bpp)))
def distance(x, y):
return Interval(abs(x - y))
net_size = BreakpointPair.net_size(bpp, distance)
self.assertEqual(Interval(-71), net_size)
self.assertEqual(sorted([SVTYPE.DEL]),
sorted(BreakpointPair.classify(bpp, distance)))
