def test_find(self):
patterns = ('at', 'gag', 'gc', 'gata')
text = 'tatatattgcgccatattagagattagatagga'
result = set()
for pattern in patterns:
occurrences = naive_find(pattern, text)
result |= set(((o, pattern) for o in occurrences))
self.assertSetEqual(result, set(aho_corrasick(patterns, text)))
def test_small(self):
patterns = ('at', 'gag', 'gc', 'gata')
text = 'tatatattgcgccatattagagattagatagga'
for pattern in patterns:
self.assertListEqual(kmp(pattern, text), naive_find(pattern, text))
def test_find(self):
text = 'tatatattgcgccatattagagattagatagga'
self.assertListEqual(naive_find('at', text), [1, 3, 5, 13, 15, 22, 27])
self.assertListEqual(naive_find('gag', text), [19])
self.assertListEqual(naive_find('gc', text), [8, 10])
self.assertListEqual(naive_find('gata', text), [26])
def test_not_find(self):
text = 'tatatattgcgccatattagagattagatagga'
self.assertListEqual(naive_find('alt', text), [])
def test_small2(self):
text = 'ctaataatg'
t = sa_preprocess(text)
self.assertListEqual(suffix_array_match('taa', t, sort=True), naive_find('taa', text))
def test_small(self):
patterns = ('at', 'gag', 'gc', 'gata')
text = 'tatatattgcgccatattagagattagatagga'
t = sa_preprocess(text)
for pattern in patterns:
self.assertListEqual(suffix_array_match(pattern, t, sort=True), naive_find(pattern, text))