def test_no_reference_obj(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'),
name=None,
reference_object='thing')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJIIIQWERTYUIOP'))
with self.assertRaises(AttributeError):
call_protein_indel(ref_translation, mut_translation)
def test_fs(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKL'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJMMM'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation == 'ref:p.K8Mfs'
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKL'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJCMMEF'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation == 'ref:p.K8Cfs'
def test_fs_with_stops(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLT*'),
name='ref')
mut_translation = Mock(
get_aa_seq=MockFunction('ASDFGHJMMMHGFTTSBF*TUHG*'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('ref:p.K8Mfs*12', notation)
def test_ins_end(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'),
name='ref')
mut_translation = Mock(
get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOPII'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('ref:p.P19ext2', notation)
def test_large_start_deletion(self):
ref_translation = Mock(
get_aa_seq=MockFunction(
'MGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPE'
'LTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKK'
'VSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSED'
'HAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMV'
'CAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLT'
'LYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEI'
'YKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGI'
'CKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSREAEAAEAEEPWGEEAREGRR'
'RGPRRESKPEEPPPPKKPALDKGLGTGQGAVSGPPRKPPGTVAGTARGPEGGSTAQVPAP'
'TASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTL'
'SFLKRQRKGL*'),
name='ref',
)
mut_translation = Mock(get_aa_seq=MockFunction(
'MRCDRKMEVAFMV'
'CAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLT'
'LYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEI'
'YKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGI'
'CKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSREAEAAEAEEPWGEEAREGRR'
'RGPRRESKPEEPPPPKKPALDKGLGTGQGAVSGPPRKPPGTVAGTARGPEGGSTAQVPAP'
'TASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTL'
'SFLKRQRKGL*'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual(
'ref:p.M1_Y227del'
'MGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPE'
'LTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKK'
'VSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSED'
'HAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSY',
notation,
)
def test_ins_start(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'),
name='ref')
mut_translation = Mock(
get_aa_seq=MockFunction('IIASDFGHJKLQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual(None, notation)
def test_transcript_name(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'),
name=None,
reference_object=Mock(name='reft'))
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJIIIQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('reft:p.K8_L9delKLinsIII', notation)
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_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'
def test_delete_start_with_rep(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDAFGHJKL'),
name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('AFGHJKL'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('ref:p.A1_D3delASD', notation)
def test_delete_single_aa_start(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'),
name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('SDFGHJKLQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('ref:p.A1delA', notation)
def test_delins(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'),
name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJIIIQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('ref:p.K8_L9delKLinsIII', notation)
def test_synonymous(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation is None
def test_fs_immeadiate_stop(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLT*'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJMMMHGFTTSBF*'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation == 'ref:p.K8Mfs*12'
def test_ins_start(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('IIASDFGHJKLQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation == 'ref:p.A1ext-2'
def test_delete_single_aa_end(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIO'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation == 'ref:p.P19delP'
def test_deletion_rep_at_breaks(self):
ref_translation = Mock(get_aa_seq=MockFunction('ABCDEFKJFEDAGFLKJ'),
name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ABCDE' 'AGFLKJ'))
notation = call_protein_indel(ref_translation, mut_translation)
self.assertEqual('ref:p.F6_D11delFKJFED', notation)
def test_deletion(self):
ref_translation = Mock(get_aa_seq=MockFunction('ASDFGHJKLQWERTYUIOP'), name='ref')
mut_translation = Mock(get_aa_seq=MockFunction('ASDFGHJQWERTYUIOP'))
notation = call_protein_indel(ref_translation, mut_translation)
assert notation == 'ref:p.K8_L9delKL'