def test_retained_intron(self):
gene = get_example_genes()['PRKCB']
reference_genome = {
gene.chr:
MockObject(seq=MockLongString(gene.seq, offset=gene.start - 1))
}
best = get_best(gene)
bpp = BreakpointPair(
Breakpoint('16', 23957049, orient='L'),
Breakpoint('16', 23957050, orient='R'),
opposing_strands=False,
stranded=False,
event_type=SVTYPE.INS,
protocol=PROTOCOL.TRANS,
untemplated_seq='A',
)
ann = Annotation(bpp, transcript1=best, transcript2=best)
ft = FusionTranscript.build(
ann,
reference_genome,
min_orf_size=300,
max_orf_cap=10,
min_domain_mapping_match=0.9,
)
assert len(ft.transcripts) == 1
print(ft.transcripts[0].splicing_pattern)
print(best.transcripts[0].splicing_pattern)
assert ft.transcripts[
0].splicing_pattern.splice_type == SPLICE_TYPE.RETAIN
def test_build_single_transcript_inversion(self):
gene = get_example_genes()['SVEP1']
reference_genome = {
gene.chr:
MockObject(seq=MockLongString(gene.seq, offset=gene.start - 1))
}
best = get_best(gene)
bpp = BreakpointPair(
Breakpoint('9', 113152627, 113152627, orient='L'),
Breakpoint('9', 113152635, 113152635, orient='L'),
opposing_strands=True,
stranded=False,
event_type=SVTYPE.INV,
protocol=PROTOCOL.GENOME,
untemplated_seq='',
)
ann = Annotation(bpp, transcript1=best, transcript2=best)
ft = FusionTranscript.build(
ann,
reference_genome,
min_orf_size=300,
max_orf_cap=10,
min_domain_mapping_match=0.9,
)
refseq = best.transcripts[0].get_seq(reference_genome)
assert len(ft.transcripts) == 1
assert ft.transcripts[0].get_seq() == refseq
def test_small_duplication(self):
bpp = BreakpointPair(
Breakpoint('6', 157100005, strand='+', orient='R'),
Breakpoint('6', 157100007, strand='+', orient='L'),
event_type=SVTYPE.DUP,
untemplated_seq='',
protocol=PROTOCOL.GENOME,
)
# annotate the breakpoint with the gene
annotations = annotate_events([bpp],
reference_genome=self.reference_genome,
annotations=self.reference_annotations)
self.assertEqual(1, len(annotations))
ann = Annotation(bpp, transcript1=self.best, transcript2=self.best)
ft = FusionTranscript.build(
ann,
self.reference_genome,
min_orf_size=300,
max_orf_cap=10,
min_domain_mapping_match=0.9,
)
ref_tx = self.best.translations[0]
fusion_tx = ft.translations[0]
# compare the fusion translation to the refernece translation to create the protein notation
ref_aa_seq = ref_tx.get_aa_seq(self.reference_genome)
call = IndelCall(ref_aa_seq, fusion_tx.get_aa_seq())
self.assertTrue(call.is_dup)
notation = call_protein_indel(ref_tx, fusion_tx, self.reference_genome)
print(notation)
self.assertEqual('ENST00000346085:p.G319dupG', notation)
def test_build_single_transcript_inversion_reverse_strand(self):
# 1:205178631R 1:205178835R inversion
bpp = BreakpointPair(
Breakpoint('1', 205178631, orient='R'),
Breakpoint('1', 205178835, orient='R'),
opposing_strands=True,
stranded=False,
event_type=SVTYPE.INV,
protocol=PROTOCOL.GENOME,
untemplated_seq='',
)
ann = Annotation(bpp, transcript1=self.best, transcript2=self.best)
ft = FusionTranscript.build(
ann,
self.reference_genome,
min_orf_size=300,
max_orf_cap=10,
min_domain_mapping_match=0.9,
)
print(ft.exons)
print(ft.break1, ft.break2)
for ex in ft.exons:
print(
ex,
len(ex),
'==>',
ft.exon_mapping.get(ex.position, None),
len(ft.exon_mapping.get(ex.position, None)),
ft.exon_number(ex),
)
# refseq = self.best.transcripts[0].get_seq(self.reference_genome)
self.assertEqual(1, len(ft.transcripts))
self.assertEqual(1860, ft.break1)
self.assertEqual(2065, ft.break2)
flatten_fusion_transcript(ft.transcripts[0]) # test no error
def test_build_single_transcript_inversion(self):
bpp = BreakpointPair(
Breakpoint('9', 113152627, 113152627, orient='L'),
Breakpoint('9', 113152635, 113152635, orient='L'),
opposing_strands=True,
stranded=False,
event_type=SVTYPE.INV,
protocol=PROTOCOL.GENOME,
untemplated_seq=''
)
ann = Annotation(bpp, transcript1=self.best, transcript2=self.best)
ft = FusionTranscript.build(
ann, self.reference_genome,
min_orf_size=300, max_orf_cap=10, min_domain_mapping_match=0.9
)
refseq = self.best.transcripts[0].get_seq(self.reference_genome)
self.assertEqual(1, len(ft.transcripts))
self.assertEqual(refseq, ft.transcripts[0].get_seq())
def test_build_single_transcript_inversion_reverse_strand(self):
print(get_example_genes().keys())
gene = get_example_genes()['DSTYK']
reference_genome = {
gene.chr:
MockObject(seq=MockLongString(gene.seq, offset=gene.start - 1))
}
best = get_best(gene)
# 1:205178631R 1:205178835R inversion
bpp = BreakpointPair(
Breakpoint('1', 205178631, orient='R'),
Breakpoint('1', 205178835, orient='R'),
opposing_strands=True,
stranded=False,
event_type=SVTYPE.INV,
protocol=PROTOCOL.GENOME,
untemplated_seq='',
)
ann = Annotation(bpp, transcript1=best, transcript2=best)
ft = FusionTranscript.build(
ann,
reference_genome,
min_orf_size=300,
max_orf_cap=10,
min_domain_mapping_match=0.9,
)
print(ft.exons)
print(ft.break1, ft.break2)
for ex in ft.exons:
print(
ex,
len(ex),
'==>',
ft.exon_mapping.get(ex.position, None),
len(ft.exon_mapping.get(ex.position, None)),
ft.exon_number(ex),
)
# refseq = best.transcripts[0].get_seq(reference_genome)
assert len(ft.transcripts) == 1
assert ft.break1 == 1860
assert ft.break2 == 2065
flatten_fusion_transcript(ft.transcripts[0]) # test no error
def test_retained_intron(self):
bpp = BreakpointPair(
Breakpoint('16', 23957049, orient='L'),
Breakpoint('16', 23957050, orient='R'),
opposing_strands=False,
stranded=False,
event_type=SVTYPE.INS,
protocol=PROTOCOL.TRANS,
untemplated_seq='A'
)
ann = Annotation(bpp, transcript1=self.best, transcript2=self.best)
ft = FusionTranscript.build(
ann, self.reference_genome,
min_orf_size=300, max_orf_cap=10, min_domain_mapping_match=0.9
)
self.assertEqual(1, len(ft.transcripts))
print(ft.transcripts[0].splicing_pattern)
print(self.best.transcripts[0].splicing_pattern)
self.assertEqual(SPLICE_TYPE.RETAIN, ft.transcripts[0].splicing_pattern.splice_type)
def test_small_duplication(self):
gene = get_example_genes()['ARID1B']
reference_annotations = {gene.chr: [gene]}
reference_genome = {
gene.chr:
MockObject(seq=MockLongString(gene.seq, offset=gene.start - 1))
}
best = get_best(gene)
bpp = BreakpointPair(
Breakpoint('6', 157100005, strand='+', orient='R'),
Breakpoint('6', 157100007, strand='+', orient='L'),
event_type=SVTYPE.DUP,
untemplated_seq='',
protocol=PROTOCOL.GENOME,
)
# annotate the breakpoint with the gene
annotations = annotate_events([bpp],
reference_genome=reference_genome,
annotations=reference_annotations)
assert len(annotations) == 1
ann = Annotation(bpp, transcript1=best, transcript2=best)
ft = FusionTranscript.build(
ann,
reference_genome,
min_orf_size=300,
max_orf_cap=10,
min_domain_mapping_match=0.9,
)
ref_tx = best.translations[0]
fusion_tx = ft.translations[0]
# compare the fusion translation to the refernece translation to create the protein notation
ref_aa_seq = ref_tx.get_aa_seq(reference_genome)
call = IndelCall(ref_aa_seq, fusion_tx.get_aa_seq())
assert call.is_dup
notation = call_protein_indel(ref_tx, fusion_tx, reference_genome)
print(notation)
assert notation == 'ENST00000346085:p.G319dupG'