def test_duplication_in_repeat(self):
ref = 'ASFHGHGSFSFSLLLLLL' 'FLLLLSFSLMVPWSFKW'
mut = 'ASFHGHGSFSFSLLLLLLL' 'FLLLLSFSLMVPWSFKW'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(18, call.nterm_aligned)
self.assertEqual(len(ref) - 13 + 1, call.cterm_aligned)
self.assertTrue(call.is_dup)
self.assertEqual('p.L18dupL', call.hgvs_protein_notation())
def test_duplication_in_repeat(self):
ref = 'ASFHGHGSFSFSLLLLLL' 'FLLLLSFSLMVPWSFKW'
mut = 'ASFHGHGSFSFSLLLLLLL' 'FLLLLSFSLMVPWSFKW'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 18
assert call.cterm_aligned == len(ref) - 13 + 1
assert call.is_dup
assert call.hgvs_protein_notation() == 'p.L18dupL'
def test_cterminal_deletion(self):
ref = 'MABCDEFGH'
mut = 'MABCDE'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(6, call.nterm_aligned)
self.assertFalse(call.cterm_aligned)
self.assertFalse(call.is_dup)
self.assertEqual('', call.ins_seq)
self.assertEqual('FGH', call.del_seq)
self.assertEqual('p.F7_H9delFGH', call.hgvs_protein_notation())
def test_insertion_in_repeat(self):
ref = 'MABCDEEEEFGH'
mut = 'MABCDEEEEEEFGH'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 9
assert call.cterm_aligned == len(call.ref_seq) - 6 + 1
assert call.is_dup
assert call.ins_seq == 'EE'
assert call.del_seq == ''
assert call.hgvs_protein_notation() == 'p.E8_E9dupEE'
def test_cterminal_no_orf_ext(self):
ref = 'MABCDEFGH'
mut = 'MABCDEFGHIJK*'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 9
assert not call.cterm_aligned
assert not call.is_dup
assert call.ins_seq == 'IJK*'
assert call.del_seq == ''
assert call.hgvs_protein_notation() == 'p.H9ext*4'
def test_cterminal_no_orf_ext(self):
ref = 'MABCDEFGH'
mut = 'MABCDEFGHIJK*'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(9, call.nterm_aligned)
self.assertFalse(call.cterm_aligned)
self.assertFalse(call.is_dup)
self.assertEqual('IJK*', call.ins_seq)
self.assertEqual('', call.del_seq)
self.assertEqual('p.H9ext*4', call.hgvs_protein_notation())
def test_deletion(self):
ref = 'MABCDEFGH'
mut = 'MABCFGH'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 4
assert call.cterm_aligned == len(call.ref_seq) - 7 + 1
assert not call.is_dup
assert call.ins_seq == ''
assert call.del_seq == 'DE'
assert call.hgvs_protein_notation() == 'p.D5_E6delDE'
def test_insertion(self):
ref = 'MABCDEFGH'
mut = 'MABCKADEFGH'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 4
assert call.cterm_aligned == len(call.ref_seq) - 5 + 1
assert not call.is_dup
assert call.ins_seq == 'KA'
assert call.del_seq == ''
assert call.hgvs_protein_notation() == 'p.C4_D5insKA'
def test_cterminal_deletion(self):
ref = 'MABCDEFGH'
mut = 'MABCDE'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 6
assert not call.cterm_aligned
assert not call.is_dup
assert call.ins_seq == ''
assert call.del_seq == 'FGH'
assert call.hgvs_protein_notation() == 'p.F7_H9delFGH'
def test_cterminal_stop_extension(self):
ref = 'MABCDEFGH*'
mut = 'MABCDEFGHIJK*'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(9, call.nterm_aligned)
self.assertFalse(call.cterm_aligned)
self.assertFalse(call.is_dup)
self.assertEqual('IJK', call.ins_seq)
self.assertEqual('', call.del_seq)
self.assertEqual('p.*10ext*3', call.hgvs_protein_notation())
def test_insertion_in_repeat(self):
ref = 'MABCDEEEEFGH'
mut = 'MABCDEEEEEEFGH'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(9, call.nterm_aligned)
self.assertEqual(len(call.ref_seq) - 6 + 1, call.cterm_aligned)
self.assertTrue(call.is_dup)
self.assertEqual('EE', call.ins_seq)
self.assertEqual('', call.del_seq)
self.assertEqual('p.E8_E9dupEE', call.hgvs_protein_notation())
def test_nterminal_deletion(self):
ref = 'MABCDEFGH'
mut = 'CDEFGH'
call = IndelCall(ref, mut)
print(call)
assert not call.nterm_aligned
assert call.cterm_aligned == len(call.ref_seq) - 4 + 1
assert not call.is_dup
assert call.ins_seq == ''
assert call.del_seq == 'MAB'
assert call.hgvs_protein_notation() == 'p.M1_B3delMAB'
def test_insertion(self):
ref = 'MABCDEFGH'
mut = 'MABCKADEFGH'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(4, call.nterm_aligned)
self.assertEqual(len(call.ref_seq) - 5 + 1, call.cterm_aligned)
self.assertFalse(call.is_dup)
self.assertEqual('KA', call.ins_seq)
self.assertEqual('', call.del_seq)
self.assertEqual('p.C4_D5insKA', call.hgvs_protein_notation())
def test_deletion(self):
ref = 'MABCDEFGH'
mut = 'MABCFGH'
call = IndelCall(ref, mut)
print(call)
self.assertEqual(4, call.nterm_aligned)
self.assertEqual(len(call.ref_seq) - 7 + 1, call.cterm_aligned)
self.assertFalse(call.is_dup)
self.assertEqual('', call.ins_seq)
self.assertEqual('DE', call.del_seq)
self.assertEqual('p.D5_E6delDE', call.hgvs_protein_notation())
def test_nterminal_deletion(self):
ref = 'MABCDEFGH'
mut = 'CDEFGH'
call = IndelCall(ref, mut)
print(call)
self.assertFalse(call.nterm_aligned)
self.assertEqual(len(call.ref_seq) - 4 + 1, call.cterm_aligned)
self.assertFalse(call.is_dup)
self.assertEqual('', call.ins_seq)
self.assertEqual('MAB', call.del_seq)
self.assertEqual('p.M1_B3delMAB', call.hgvs_protein_notation())
def test_cterminal_stop_extension(self):
ref = 'MABCDEFGH*'
mut = 'MABCDEFGHIJK*'
call = IndelCall(ref, mut)
print(call)
assert call.nterm_aligned == 9
assert not call.cterm_aligned
assert not call.is_dup
assert call.ins_seq == 'IJK'
assert call.del_seq == ''
assert call.hgvs_protein_notation() == 'p.*10ext*3'
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_deletion(self):
refseq = 'asdfghjkl'
mutseq = 'asdfkl'
indel = IndelCall(refseq, mutseq)
assert indel.nterm_aligned == 4
assert indel.cterm_aligned == len(indel.ref_seq) - 8 + 1
assert indel.del_seq == 'ghj'
assert indel.ins_seq == ''
assert not indel.is_dup
def test_delete_end(self):
refseq = 'asdfghjkl'
mutseq = 'asdfgh'
indel = IndelCall(refseq, mutseq)
self.assertEqual(6, indel.last_aligned)
self.assertEqual(-1, indel.next_aligned)
self.assertEqual('jkl', indel.del_seq)
self.assertEqual('', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_deletion(self):
refseq = 'asdfghjkl'
mutseq = 'asdfkl'
indel = IndelCall(refseq, mutseq)
self.assertEqual(4, indel.last_aligned)
self.assertEqual(8, indel.next_aligned)
self.assertEqual('ghj', indel.del_seq)
self.assertEqual('', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_ins_end(self):
refseq = 'asdfghjkl'
mutseq = 'asdfghjklmmm'
indel = IndelCall(refseq, mutseq)
assert indel.nterm_aligned == 9
assert indel.cterm_aligned == 0
assert indel.del_seq == ''
assert indel.ins_seq == 'mmm'
assert not indel.is_dup
def test_delins_start(self):
refseq = 'asdfghjkl'
mutseq = 'mmfghjkl'
indel = IndelCall(refseq, mutseq)
self.assertEqual(0, indel.nterm_aligned)
self.assertEqual(6, indel.cterm_aligned)
self.assertEqual('asd', indel.del_seq)
self.assertEqual('mm', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_ins_end(self):
refseq = 'asdfghjkl'
mutseq = 'asdfghjklmmm'
indel = IndelCall(refseq, mutseq)
self.assertEqual(9, indel.nterm_aligned)
self.assertEqual(0, indel.cterm_aligned)
self.assertEqual('', indel.del_seq)
self.assertEqual('mmm', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_deletion(self):
refseq = 'asdfghjkl'
mutseq = 'asdfkl'
indel = IndelCall(refseq, mutseq)
self.assertEqual(4, indel.nterm_aligned)
self.assertEqual(len(indel.ref_seq) - 8 + 1, indel.cterm_aligned)
self.assertEqual('ghj', indel.del_seq)
self.assertEqual('', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_delete_start_repetition(self):
refseq = 'asdafghjkl'
mutseq = 'afghjkl'
indel = IndelCall(refseq, mutseq)
self.assertEqual(0, indel.nterm_aligned)
self.assertEqual(7, indel.cterm_aligned)
self.assertEqual('asd', indel.del_seq)
self.assertEqual('', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_delete_end(self):
refseq = 'asdfghjkl'
mutseq = 'asdfgh'
indel = IndelCall(refseq, mutseq)
assert indel.nterm_aligned == 6
assert indel.cterm_aligned == 0
assert indel.del_seq == 'jkl'
assert indel.ins_seq == ''
assert not indel.is_dup
def test_ins_start(self):
refseq = 'asdfghjkl'
mutseq = 'mmasdfghjkl'
indel = IndelCall(refseq, mutseq)
self.assertEqual(-1, indel.last_aligned)
self.assertEqual(1, indel.next_aligned)
self.assertEqual('', indel.del_seq)
self.assertEqual('mm', indel.ins_seq)
self.assertFalse(indel.is_dup)
def test_delete_start_repetition(self):
refseq = 'asdafghjkl'
mutseq = 'afghjkl'
indel = IndelCall(refseq, mutseq)
assert indel.nterm_aligned == 0
assert indel.cterm_aligned == 7
assert indel.del_seq == 'asd'
assert indel.ins_seq == ''
assert not indel.is_dup
def test_delins_start(self):
refseq = 'asdfghjkl'
mutseq = 'mmfghjkl'
indel = IndelCall(refseq, mutseq)
assert indel.nterm_aligned == 0
assert indel.cterm_aligned == 6
assert indel.del_seq == 'asd'
assert indel.ins_seq == 'mm'
assert not indel.is_dup
def test_dup(self):
refseq = 'asdfghjkl'
mutseq = 'asdfsdfghjkl'
indel = IndelCall(refseq, mutseq)
print(indel)
self.assertEqual(4, indel.nterm_aligned)
self.assertEqual(len(indel.ref_seq) - 2 + 1, indel.cterm_aligned)
self.assertEqual('', indel.del_seq)
self.assertEqual('sdf', indel.ins_seq)
self.assertTrue(indel.is_dup)
