from tests.compat import unittest, mock from fuzzysearch.common import Match, get_best_match_in_group, group_matches from fuzzysearch.levenshtein import find_near_matches_levenshtein, \ find_near_matches_levenshtein_linear_programming as fnm_levenshtein_lp from fuzzysearch.levenshtein_ngram import _expand, \ find_near_matches_levenshtein_ngrams as fnm_levenshtein_ngrams class TestFuzzySearch(unittest.TestCase): def test_empty_sequence(self): self.assertEqual( list(fnm_levenshtein_lp('PATTERN', '', max_l_dist=0)), [], ) def test_empty_subsequence_exeption(self): with self.assertRaises(ValueError): list(fnm_levenshtein_lp('', 'TEXT', max_l_dist=0)) 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_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) #self.assertEqual([Match(start=4, end=7, dist=0)], 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), matches) #self.assertEqual([Match(start=1, end=5, 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) class TestExpand(unittest.TestCase): def test_both_empty(self): self.assertEqual(_expand('', '', 0), (0, 0)) def test_empty_subsequence(self): self.assertEqual(_expand('', 'TEXT', 0), (0, 0)) def test_empty_sequence(self): self.assertEqual(_expand('PATTERN', '', 0), (None, None)) def test_identical(self): self.assertEqual(_expand('abc', 'abc', 0), (0, 3)) self.assertEqual(_expand('abc', 'abc', 1), (0, 3)) self.assertEqual(_expand('abc', 'abc', 2), (0, 3)) def test_first_item_missing(self): self.assertEqual(_expand('abcd', 'bcd', 0), (None, None)) self.assertEqual(_expand('abcd', 'bcd', 1), (1, 3)) self.assertEqual(_expand('abcd', 'bcd', 2), (1, 3)) def test_second_item_missing(self): self.assertEqual(_expand('abcd', 'acd', 0), (None, None)) self.assertEqual(_expand('abcd', 'acd', 1), (1, 3)) self.assertEqual(_expand('abcd', 'acd', 2), (1, 3)) def test_second_before_last_item_missing(self): self.assertEqual(_expand('abcd', 'abd', 0), (None, None)) self.assertEqual(_expand('abcd', 'abd', 1), (1, 3)) self.assertEqual(_expand('abcd', 'abd', 2), (1, 3)) def test_last_item_missing(self): self.assertEqual(_expand('abcd', 'abc', 0), (None, None)) self.assertEqual(_expand('abcd', 'abc', 1), (1, 3)) self.assertEqual(_expand('abcd', 'abc', 2), (1, 3)) def test_completely_different(self): self.assertEqual(_expand('abc', 'def', 0), (None, None)) def test_startswith(self): self.assertEqual(_expand('abc', 'abcd', 0), (0, 3)) self.assertEqual(_expand('abc', 'abcd', 1), (0, 3)) self.assertEqual(_expand('abc', 'abcd', 2), (0, 3)) class TestFindNearMatchesLevenshteinBase(object): def search(self, subsequence, sequence, max_l_dist): raise NotImplementedError def test_empty_sequence(self): self.assertEqual(self.search('PATTERN', '', max_l_dist=0), []) def test_empty_subsequence_exeption(self): with self.assertRaises(ValueError): self.search('', 'TEXT', max_l_dist=0) def test_match_identical_sequence(self): self.assertEqual( self.search('PATTERN', 'PATTERN', max_l_dist=0), [Match(start=0, end=len('PATTERN'), dist=0)], ) def test_substring(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTERNaaaaaaaaa' expected_match = Match(start=10, end=17, dist=0) self.assertEqual( self.search(substring, text, max_l_dist=1), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=0), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=2), [expected_match], ) def test_double_first_item(self): self.assertEqual( self.search('def', 'abcddefg', max_l_dist=1), [Match(start=4, end=7, dist=0)], ) def test_double_last_item(self): self.assertEqual( self.search('def', 'abcdeffg', max_l_dist=1), [Match(start=3, end=6, dist=0)], ) def test_double_first_items(self): self.assertEqual( self.search('defgh', 'abcdedefghi', max_l_dist=3), [Match(start=5, end=10, dist=0)], ) def test_double_last_items(self): self.assertEqual( self.search('cdefgh', 'abcdefghghi', max_l_dist=3), [Match(start=2, end=8, dist=0)], ) def test_missing_second_item(self): self.assertEqual( self.search('bde', 'abcdefg', max_l_dist=1), [Match(start=1, end=5, dist=1)], ) def test_missing_second_to_last_item(self): self.assertEqual( self.search('bce', 'abcdefg', max_l_dist=1), [Match(start=1, end=5, dist=1)], ) self.assertEqual( self.search('bce', 'abcdefg', max_l_dist=2), [Match(start=1, end=5, dist=1)], ) def test_one_missing_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATERNaaaaaaaaa' expected_match = Match(start=10, end=16, dist=1) self.assertEqual( self.search(substring, text, max_l_dist=0), [], ) self.assertEqual( self.search(substring, text, max_l_dist=1), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=2), [expected_match], ) def test_one_changed_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATtERNaaaaaaaaa' expected_match = Match(start=10, end=17, dist=1) self.assertEqual( self.search(substring, text, max_l_dist=0), [], ) self.assertEqual( self.search(substring, text, max_l_dist=1), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=2), [expected_match], ) def test_one_extra_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTXERNaaaaaaaaa' expected_match = Match(start=10, end=18, dist=1) self.assertEqual( self.search(substring, text, max_l_dist=0), [], ) self.assertEqual( self.search(substring, text, max_l_dist=1), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=2), [expected_match], ) def test_one_extra_repeating_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTTERNaaaaaaaaa' expected_match = Match(start=10, end=18, dist=1) self.assertEqual( self.search(substring, text, max_l_dist=0), [], ) self.assertEqual( self.search(substring, text, max_l_dist=1), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=2), [expected_match], ) def test_one_extra_repeating_at_end(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTERNNaaaaaaaaa' expected_match = Match(start=10, end=17, dist=0) self.assertEqual( self.search(substring, text, max_l_dist=0), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=1), [expected_match], ) self.assertEqual( self.search(substring, text, max_l_dist=2), [expected_match], ) def test_one_missing_at_end_of_sequence(self): self.assertEqual( self.search('defg', 'abcdef', max_l_dist=1), [Match(3, 6, 1)], ) def test_dna_search(self): # see: http://stackoverflow.com/questions/19725127/ text = ''.join('''\ GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGT CACACACACATTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACAC ATTAGACGCGTACATAGACACAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATAC TCGCGTAGTCGTGGGAGGCAAGGCACACAGGGGATAGG '''.split()) pattern = 'TGCACTGTAGGGATAACAAT' self.assertEqual( self.search(pattern, text, max_l_dist=2), [Match(start=3, end=24, dist=1)], ) def test_protein_search1(self): # see: # * BioPython archives from March 14th, 2014 # http://lists.open-bio.org/pipermail/biopython/2014-March/009030.html # * https://github.com/taleinat/fuzzysearch/issues/3 text = ''.join('''\ XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAGGGTTLTTSSAAAAAAAAAAAA AAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS '''.split()) pattern = "GGGTTLTTSS" self.assertEqual( self.search(pattern, text, max_l_dist=2), [Match(start=19, end=29, dist=1), Match(start=42, end=52, dist=0), Match(start=99, end=109, dist=0)], ) def test_protein_search2(self): # see: # * BioPython archives from March 14th, 2014 # http://lists.open-bio.org/pipermail/biopython/2014-March/009030.html # * https://github.com/taleinat/fuzzysearch/issues/3 text = ''.join('''\ XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAGGGTTVTTSSAAAAAAAAAAA AAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS '''.split()) pattern = "GGGTTLTTSS" self.assertEqual( self.search(pattern, text, max_l_dist=2), [Match(start=19, end=29, dist=1), Match(start=42, end=52, dist=1), Match(start=99, end=109, dist=0)], ) class TestFindNearMatchesLevenshteinNgrams(TestFindNearMatchesLevenshteinBase, unittest.TestCase): def search(self, subsequence, sequence, max_l_dist): return fnm_levenshtein_ngrams(subsequence, sequence, max_l_dist) class TestFindNearMatchesLevenshteinLP(TestFindNearMatchesLevenshteinBase, unittest.TestCase): 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) ) ] class TestFindNearMatchesLevenshtein(TestFindNearMatchesLevenshteinBase, unittest.TestCase): def search(self, subsequence, sequence, max_l_dist): return find_near_matches_levenshtein(subsequence, sequence, max_l_dist) def test_fallback_to_search_exact(self): with mock.patch('fuzzysearch.levenshtein.search_exact') \ as mock_search_exact: mock_search_exact.return_value = [7] matches = find_near_matches_levenshtein('a', 'b' * 10, 0) self.assertGreater(mock_search_exact.call_count, 0) self.assertEqual(matches, [Match(7, 8, 0)])