def trans_window_setup():
n = argparse.Namespace()
gene = Gene('1', 1, 9999, name='KRAS', strand=STRAND.POS)
n.pre_transcript = PreTranscript(
gene=gene, exons=[(1001, 1100), (1401, 1500), (1701, 1750), (3001, 4000)]
)
gene.unspliced_transcripts.append(n.pre_transcript)
for spl in n.pre_transcript.generate_splicing_patterns():
n.pre_transcript.transcripts.append(Transcript(n.pre_transcript, spl))
n.annotations = {gene.chr: [gene]}
n.genome_evidence = MockObject(
annotations={},
read_length=100,
max_expected_fragment_size=550,
config={**DEFAULTS, 'validate.call_error': 11},
)
n.trans_evidence = MockObject(
annotations={},
read_length=100,
max_expected_fragment_size=550,
overlapping_transcripts={n.pre_transcript},
config={**DEFAULTS, 'validate.call_error': 11},
)
setattr(
n.trans_evidence,
'_select_transcripts',
lambda *pos: n.trans_evidence.overlapping_transcripts,
)
setattr(
n.trans_evidence,
'traverse',
partial(TranscriptomeEvidence.traverse, n.trans_evidence),
)
return n
def setUp(self):
gene = Gene('1', 1, 9999, name='KRAS', strand=STRAND.POS)
self.pre_transcript = PreTranscript(gene=gene,
exons=[(1001, 1100), (1401, 1500),
(1701, 1750), (3001, 4000)])
gene.unspliced_transcripts.append(self.pre_transcript)
for spl in self.pre_transcript.generate_splicing_patterns():
self.pre_transcript.transcripts.append(
Transcript(self.pre_transcript, spl))
self.annotations = {gene.chr: [gene]}
self.genome_evidence = MockObject(annotations={},
read_length=100,
max_expected_fragment_size=550,
call_error=11)
self.trans_evidence = MockObject(
annotations={},
read_length=100,
max_expected_fragment_size=550,
call_error=11,
overlapping_transcripts={self.pre_transcript},
)
setattr(
self.trans_evidence,
'_select_transcripts',
lambda *pos: self.trans_evidence.overlapping_transcripts,
)
setattr(
self.trans_evidence,
'traverse',
partial(TranscriptomeEvidence.traverse, self.trans_evidence),
)
def test_shift_overaligned_left(self):
# qwertyuiopasdf---kkkkkdf------ghjklzxcvbnm
# .......... ................
gene = Gene('1', 1, 1000, strand='+')
transcript = PreTranscript(exons=[(1, 14), (22, 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('12=7D14='),
query_sequence='qwertyuiopasdfghjklzxcvbnm',
)
evidence = TranscriptomeEvidence(
annotations={},
reference_genome={'1': MockObject(seq='qwertyuiopasdfkkkkkdfghjklzxcvbnmsbcdefhi')},
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('14=7N12=')
def test_many_small_exons(self):
g = Gene('fake', 17271277, 17279592, strand='+')
pre_transcript = PreTranscript(
gene=g,
exons=[
(17271277, 17271984),
(17272649, 17272709),
(17275586, 17275681),
(17275769, 17275930),
(17276692, 17276817),
(17277168, 17277388), # 220
(17277845, 17277888), # 44
(17278293, 17278378), # 86
(17279229, 17279592) # 364
])
g.transcripts.append(pre_transcript)
for patt in pre_transcript.generate_splicing_patterns():
pre_transcript.transcripts.append(Transcript(pre_transcript, patt))
b = Breakpoint(chr='fake', start=17279591, orient=ORIENT.LEFT)
self.assertEqual(Interval(17277321, 17279701),
self.transcriptome_window(b, [pre_transcript]))