def test_simple_amino(self):
simple_result = pattern_search.SimpleAmino('A')
assert simple_result.amino == 'A'
with self.assertRaisesRegex(ValueError, 'Invalid amino acid'):
pattern_search.SimpleAmino('B')
assert simple_result.match('A')
assert not simple_result.match('C')
def test_offset_ok_element(self):
sequence = 'MAGICHAT'
simple_amino = pattern_search.SimpleAmino('A')
assert simple_amino.offset_ok(sequence, 0)
assert not simple_amino.offset_ok(sequence, 8)
simple_with_repeats = pattern_search.SimpleAmino('A(2)')
assert simple_with_repeats.offset_ok(sequence, 0)
assert not simple_with_repeats.offset_ok(sequence, 8)
def test_offset_ok_element_cterm(self):
sequence = 'MAGICHAT'
simple_cterm = pattern_search.SimpleAmino('M', cterm=True)
assert simple_cterm.offset_ok(sequence, 7)
assert not simple_cterm.offset_ok(sequence, 6)
cterm_with_repeats = pattern_search.SimpleAmino('M(2)', cterm=True)
assert cterm_with_repeats.offset_ok(sequence, 7)
assert cterm_with_repeats.offset_ok(sequence, 6)
assert not cterm_with_repeats.offset_ok(sequence, 2)
cterm_range = pattern_search.SimpleAmino('M(1,4)', cterm=True)
assert cterm_range.offset_ok(sequence, 7)
assert cterm_range.offset_ok(sequence, 4)
assert not cterm_range.offset_ok(sequence, 0)
def test_match_with_next(self):
simple_amino = pattern_search.SimpleAmino('A')
any_amino = pattern_search.AnyAmino('x', simple_amino)
assert any_amino.match_including_following('MAGICHAT')
assert any_amino.match_including_following('MAGICHAT').distance == 2
assert any_amino.match_including_following('MAGICHAT', 5)
def test_match_all_lengths_03(self):
sequence = 'AAATAAAA'
multi_a_1 = pattern_search.SimpleAmino('A(0,3)')
simple_t = pattern_search.SimpleAmino('T', multi_a_1)
multi_a_2 = pattern_search.SimpleAmino('A(0,3)', simple_t)
assert len(multi_a_2.match_all_possible(sequence)) == 4
def test_match_all_lengths_04(self):
sequence = 'MAAAAGIC'
multiple_as = pattern_search.SimpleAmino('A(0,4)')
simple_m = pattern_search.SimpleAmino('M', multiple_as)
assert len(simple_m.match_all_possible(sequence)) == 5
def test_match_all_lengths_12(self):
sequence = 'MAAGGIC'
multiple_as = pattern_search.SimpleAmino(
'A(1,2)', pattern_search.SimpleAmino('G(1,2)'))
simple_m = pattern_search.SimpleAmino('M', multiple_as)
assert len(simple_m.match_all_possible(sequence)) == 2