def test_dna_search(self):
# see: http://stackoverflow.com/questions/19725127/
text = ''.join('''\
GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGT
CACACACACATTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACAC
ATTAGACGCGTACATAGACACAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATAC
TCGCGTAGTCGTGGGAGGCAAGGCACACAGGGGATAGG
'''.split())
pattern = 'TGCACTGTAGGGATAACAAT'
matches = list(fnm_levenshtein_lp(pattern, text, max_l_dist=2))
self.assertTrue(len(matches) > 0)
self.assertIn(Match(start=3, end=24, dist=1), matches)
def test_dna_search(self):
# see: http://stackoverflow.com/questions/19725127/
text = ''.join('''\
GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGT
CACACACACATTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACAC
ATTAGACGCGTACATAGACACAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATAC
TCGCGTAGTCGTGGGAGGCAAGGCACACAGGGGATAGG
'''.split())
pattern = 'TGCACTGTAGGGATAACAAT'
matches = list(fnm_levenshtein_lp(pattern, text, max_l_dist=2))
self.assertTrue(len(matches) > 0)
self.assertIn(Match(start=3, end=24, dist=1), matches)
def test_missing_second_item(self):
sequence = 'abcdefg'
pattern = 'bde'
matches = \
list(fnm_levenshtein_lp(pattern, sequence, max_l_dist=1))
self.assertIn(Match(start=1, end=5, dist=1, matched='bcde'), matches)
def search(self, subsequence, sequence, max_l_dist):
return consolidate_overlapping_matches(
fnm_levenshtein_lp(subsequence, sequence, max_l_dist)
)
def test_double_first_item(self):
sequence = 'abcddefg'
pattern = 'def'
matches = \
list(fnm_levenshtein_lp(pattern, sequence, max_l_dist=1))
self.assertIn(Match(start=4, end=7, dist=0, matched=pattern), matches)
def test_match_identical_sequence(self):
matches = \
list(fnm_levenshtein_lp('PATTERN', 'PATTERN', max_l_dist=0))
self.assertEqual(matches, [Match(start=0, end=len('PATTERN'), dist=0,
matched='PATTERN')])
def test_empty_subsequence_exeption(self):
with self.assertRaises(ValueError):
list(fnm_levenshtein_lp('', 'TEXT', max_l_dist=0))
def test_empty_sequence(self):
self.assertEqual(
list(fnm_levenshtein_lp('PATTERN', '', max_l_dist=0)),
[],
)
def search(self, subsequence, sequence, max_l_dist):
return [
get_best_match_in_group(group) for group in group_matches(
fnm_levenshtein_lp(subsequence, sequence, max_l_dist))
]
def test_missing_second_item(self):
sequence = 'abcdefg'
pattern = 'bde'
matches = \
list(fnm_levenshtein_lp(pattern, sequence, max_l_dist=1))
self.assertIn(Match(start=1, end=5, dist=1), matches)
def search(self, subsequence, sequence, max_l_dist):
return consolidate_overlapping_matches(
fnm_levenshtein_lp(subsequence, sequence, max_l_dist)
)
def test_double_first_item(self):
sequence = 'abcddefg'
pattern = 'def'
matches = \
list(fnm_levenshtein_lp(pattern, sequence, max_l_dist=1))
self.assertIn(Match(start=4, end=7, dist=0), matches)
def test_match_identical_sequence(self):
matches = \
list(fnm_levenshtein_lp('PATTERN', 'PATTERN', max_l_dist=0))
self.assertEqual(matches, [Match(start=0, end=len('PATTERN'), dist=0)])
def test_empty_subsequence_exeption(self):
with self.assertRaises(ValueError):
list(fnm_levenshtein_lp('', 'TEXT', max_l_dist=0))
def test_empty_sequence(self):
self.assertEqual(
list(fnm_levenshtein_lp('PATTERN', '', max_l_dist=0)),
[],
)
