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_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_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_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_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_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_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_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_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_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_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_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_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_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())