def test_find_optional_simple(self):
sequence = 'MYKITTYYYY'
pattern = pattern_search.Pattern('T-Y(0,1).')
assert pattern.find(sequence) == 4
pattern = pattern_search.Pattern('K-Y(0,1)-I.')
assert pattern.find(sequence) == 2
def test_find_all_start(self):
sequence = 'TAAATAAAATA'
pattern = pattern_search.Pattern('<T.')
assert len(pattern.find_all(sequence)) == 1
pattern = pattern_search.Pattern('<T-A(0,3).')
assert len(pattern.find_all(sequence)) == 4
def test_find_all_end(self):
sequence = 'TAAATAAAATA'
pattern = pattern_search.Pattern('A>.')
assert len(pattern.find_all(sequence)) == 1
pattern = pattern_search.Pattern('A(0,3)-T-A>.')
assert len(pattern.find_all('TAAATAAAATA')) == 4
def test_find_range_any(self):
sequence = 'MYKITTYYYY'
pattern = pattern_search.Pattern('x(2,3).')
assert pattern.find(sequence) == 0
pattern = pattern_search.Pattern('K-x(0,1)-I.')
assert pattern.find(sequence) == 2
def test_find_any_repeats(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('M-x-x-x-C.')
assert pattern.find(sequence) == 0
pattern = pattern_search.Pattern('M-x(3)-C.')
assert pattern.find(sequence) == 0
def test_find_all_basic_types(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('x(3).')
assert len(pattern.find_all(sequence)) == 6
pattern = pattern_search.Pattern('[MH]-[AGI](0,3).')
assert len(pattern.find_all(sequence)) == 6
pattern = pattern_search.Pattern('{AG}(1,3).')
assert len(pattern.find_all(sequence)) == 8
def test_find_negated(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('{A}.')
assert pattern.find(sequence) == 0
assert pattern.find('A') == -1
assert pattern.find('') == -1
pattern = pattern_search.Pattern('{MAGIC}.')
assert pattern.find(sequence) == 5
assert pattern.find('MAGIC') == -1
assert pattern.find('GAMMA') == -1
def test_find_range_simple(self):
sequence = 'MYKITTYYYY'
pattern = pattern_search.Pattern('Y(1,2).')
assert pattern.find(sequence) == 1
pattern = pattern_search.Pattern('Y(2,4).')
assert pattern.find(sequence) == 6
pattern = pattern_search.Pattern('T(2,3)-Y.')
assert pattern.find(sequence) == 4
def test_optional_cterminus_repeat(self):
pattern = pattern_search.Pattern('A-[T>](1,2).')
assert pattern.find('MAGICHAT') == 6
hits = pattern.find_all('MAGICHAT')
assert len(hits) == 1
assert hits[0].start == 6 and hits[0].end == 8
assert "MAGICHAT"[hits[0].start:hits[0].end] == "AT"
pattern = pattern_search.Pattern('[T>](1,2).')
assert pattern.find('MAGICHAT') == 7
assert len(pattern.find_all('MAGICHAT')) == 1
def test_find_any_combos(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('x-A.')
assert pattern.find('A') == -1
assert pattern.find('') == -1
assert pattern.find('AC') == -1
assert pattern.find(sequence) == 0
# three-letter combinations:
pattern = pattern_search.Pattern('x-A-x.')
assert pattern.find(sequence) == 0
assert pattern.find('A') == -1
def test_find_multiple(self):
sequence = 'MAGICHAT'
# simplest but inefficient: one acceptable amino acid
pattern = pattern_search.Pattern('[A].')
assert pattern.find(sequence) == 1
assert pattern.find('M') == -1
assert pattern.find('') == -1
# actual use case: multiple acceptable amino acids
pattern = pattern_search.Pattern('[AC].')
# This finds an A...
assert pattern.find(sequence) == 1
# ...or a C
assert pattern.find('CAT') == 0
assert pattern.find('KITTY') == -1
def test_find_single_then_any(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('M-x.')
assert pattern.find('M') == -1
assert pattern.find('') == -1
assert pattern.find('AM') == -1
assert pattern.find(sequence) == 0
def test_find(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('Y.')
assert pattern.find(sequence) == -1
pattern = pattern_search.Pattern('A.')
assert pattern.find(sequence) == 1
pattern = pattern_search.Pattern('A-G.')
assert pattern.find(sequence) == 1
pattern = pattern_search.Pattern('A-Y.')
assert pattern.find(sequence) == -1
pattern = pattern_search.Pattern('A-T.')
assert pattern.find(sequence) == 6
assert pattern.find('') == -1
def test_distance(self):
pattern = pattern_search.Pattern('M-A-G-I-C.')
result = pattern.find_all('MAGICHAT')
assert result[0].end == 5
assert len(result[0]) == 5
result = pattern.find_all('AMAGICHAT')
assert result[0].end == 6
assert len(result[0]) == 5
def test_termini(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('<M.')
assert pattern.find(sequence) == 0
assert pattern.find('AMAGICHAT') == -1
pattern = pattern_search.Pattern('T>.')
assert pattern.find(sequence) == 7
assert pattern.find('MAGICHATS') == -1
pattern = pattern_search.Pattern('<M-x(6)-T>.')
assert pattern.find(sequence) == 0
assert pattern.find('MAGICHATS') == -1
assert pattern.find('AMAGICHAT') == -1
sequence = 'MMMCHEESE'
pattern = pattern_search.Pattern('<M(3).')
assert pattern.find(sequence) == 0
pattern = pattern_search.Pattern('<M(3,4).')
assert pattern.find(sequence) == 0
pattern = pattern_search.Pattern('Y(2,3)>.')
assert pattern.find('KITTYYY') == 4
def test_invalid_pattern(self):
with self.assertRaises(ValueError):
pattern_search.Pattern('AA.')
with self.assertRaises(ValueError):
pattern_search.Pattern('*.')
def test_multiple_start(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('<[MA].')
assert len(pattern.find_all(sequence)) == 1
def test_leading_multiple_repeats(self):
sequence = 'MMAGIC'
result = pattern_search.Pattern(
'M(1,2)-A(0,1).').head.match_all_possible(sequence)
assert len(result) == 3
def test_invalid_optional_or_cterm(self):
with self.assertRaises(ValueError):
pattern_search.Pattern('A>-[T>].')
with self.assertRaises(ValueError):
pattern_search.Pattern('A>-C-[T>].')
def test_find_all_range_not_start(self):
assert len(pattern_search.Pattern('<{G}(1,3).').find_all('MAGIC')) == 2
def test_find_all_range_not_end(self):
assert len(
pattern_search.Pattern('{H}(1,3)>.').find_all('MAGICHAT')) == 2
def test_negated_end(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('{D}>.')
assert len(pattern.find_all(sequence)) == 1
def test_negated_start(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('<{N}.')
assert len(pattern.find_all(sequence)) == 1
def test_find_all_range_multi_start(self):
assert len(
pattern_search.Pattern('<[MA](1,3).').find_all('MAGIC')) == 2
def test_find_all_range_multi_end(self):
assert len(
pattern_search.Pattern('[AT](1,3)>.').find_all('MAGICHAT')) == 2
def test_find_all_leading_multiple_repeats(self):
sequence = 'MMAGIC'
result = pattern_search.Pattern('M(1,2)-A(0,1).').find_all(sequence)
assert len(result) == 5
def test_multiple_end(self):
sequence = 'MAGICHAT'
pattern = pattern_search.Pattern('[AT]>.')
assert len(pattern.find_all(sequence)) == 1
def test_find_all_range_start(self):
pattern = pattern_search.Pattern('<M(1,3).')
assert len(pattern.find_all('MMAGIC')) == 2
def test_find_all_range_end(self):
sequence = 'KITTYYYY'
pattern = pattern_search.Pattern('Y(2,5)>.')
assert len(pattern.find_all(sequence)) == 3
def test_find_all_multiple_repeats(self):
sequence = 'AAATAAAA'
pattern = pattern_search.Pattern('A(0,3)-T-A(0,3).')
assert len(pattern.find_all(sequence)) == 16
