def test_shift_overaligned(self):
# qwertyuiopas---kkkkk------dfghjklzxcvbnm
# .......... ................
gene = Gene('1', 1, 1000, strand='+')
transcript = PreTranscript(exons=[(1, 12), (20, 28)], gene=gene, strand='+')
for spl_patt in transcript.generate_splicing_patterns():
transcript.transcripts.append(Transcript(transcript, spl_patt))
gene.transcripts.append(transcript)
read = SamRead(
reference_name='1',
reference_start=0,
cigar=_cigar.convert_string_to_cigar('14=7D12='),
query_sequence='qwertyuiopasdfghjklzxcvbnm',
)
evidence = TranscriptomeEvidence(
annotations={},
reference_genome={'1': MockObject(seq='qwertyuiopasdfkkkkkdfghjklzxcvbnm')},
bam_cache=MockObject(get_read_reference_name=lambda r: r.reference_name),
break1=Breakpoint('1', 1, orient='L', strand='+'),
break2=Breakpoint('1', 10, orient='R', strand='+'),
read_length=75,
stdev_fragment_size=75,
median_fragment_size=220,
)
evidence.overlapping_transcripts.add(transcript)
new_read = evidence.standardize_read(read)
assert new_read.cigar == _cigar.convert_string_to_cigar('12=7N14=')
def setUp(self):
b1 = Breakpoint('1', 1051, 1051, 'L')
b2 = Breakpoint('1', 1551, 1551, 'R')
self.read_length = 50
self.trans_ev = TranscriptomeEvidence(
{}, # fake the annotations
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1,
)
self.genomic_ev = GenomeEvidence(
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1,
)
class TestComputeFragmentSizes(unittest.TestCase):
def setUp(self):
b1 = Breakpoint('1', 1051, 1051, 'L')
b2 = Breakpoint('1', 1551, 1551, 'R')
self.read_length = 50
self.trans_ev = TranscriptomeEvidence(
{}, # fake the annotations
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1,
)
self.genomic_ev = GenomeEvidence(
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1)
def test_genomic_vs_trans_no_annotations(self):
# should be identical
read, mate = mock_read_pair(
MockRead('name',
'1',
1051 - self.read_length + 1,
1051,
is_reverse=False),
MockRead('name',
'1',
2300,
2300 + self.read_length - 1,
is_reverse=True))
self.assertEqual(self.trans_ev.compute_fragment_size(read, mate),
self.genomic_ev.compute_fragment_size(read, mate))
def test_reverse_reads(self):
read, mate = mock_read_pair(
MockRead('name', '1', 1001, 1100, is_reverse=False),
MockRead('name', '1', 2201, 2301, is_reverse=True))
self.assertEqual(Interval(1300),
self.genomic_ev.compute_fragment_size(read, mate))
self.assertEqual(Interval(1300),
self.genomic_ev.compute_fragment_size(mate, read))
self.assertEqual(Interval(1300),
self.trans_ev.compute_fragment_size(read, mate))
self.assertEqual(Interval(1300),
self.trans_ev.compute_fragment_size(mate, read))
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_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(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_shift_no_transcripts(self):
read = SamRead(reference_name='1',
reference_start=0,
cigar=_cigar.convert_string_to_cigar('14=7D18='),
query_sequence='qwertyuiopasdfdfghjklzxcvbnm')
evidence = TranscriptomeEvidence(
annotations={},
reference_genome={
'1': MockObject(seq='qwertyuiopasdfkkkkkdfghjklzxcvbnm')
},
bam_cache=None,
break1=Breakpoint('1', 1, orient='L', strand='+'),
break2=Breakpoint('1', 10, orient='R', strand='+'),
read_length=75,
stdev_fragment_size=75,
median_fragment_size=220)
new_cigar = evidence.exon_boundary_shift_cigar(read)
self.assertEqual(_cigar.convert_string_to_cigar('14=7D18='), new_cigar)
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 trans_evidence(read_length):
return TranscriptomeEvidence(
{}, # fake the annotations
Breakpoint('1', 1051, 1051, 'L'),
Breakpoint('1', 1551, 1551, 'R'),
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=read_length,
stdev_fragment_size=100,
median_fragment_size=100,
config={'validate.stdev_count_abnormal': 1},
)
def transcriptome_window(ev, breakpoint, transcripts=None):
if transcripts:
ev.overlapping_transcripts.update(transcripts)
return TranscriptomeEvidence.generate_window(ev, breakpoint)
def egfr_distance(self, pos1, pos2):
return TranscriptomeEvidence.distance(self.evidence, pos1, pos2)
def transcriptome_window(self, breakpoint, transcripts=None):
if transcripts:
self.trans_evidence.overlapping_transcripts.update(transcripts)
return TranscriptomeEvidence.generate_window(self.trans_evidence,
breakpoint)
