from tests.compat import unittest from fuzzysearch.fuzzysearch import find_near_matches, Match, _expand,\ find_near_matches_with_ngrams, get_best_match_in_group, group_matches class TestFuzzySearch(unittest.TestCase): def test_empty_sequence(self): self.assertEquals([], list(find_near_matches('PATTERN', ''))) def test_empty_subsequence_exeption(self): with self.assertRaises(ValueError): list(find_near_matches('', 'TEXT')) def test_match_identical_sequence(self): matches = list(find_near_matches('PATTERN', 'PATTERN', max_l_dist=0)) self.assertEquals([Match(start=0, end=len('PATTERN'), dist=0)], matches) def test_double_first_item(self): sequence = 'abcddefg' pattern = 'def' matches = list(find_near_matches(pattern, sequence, max_l_dist=1)) self.assertIn(Match(start=4, end=7, dist=0), matches) #self.assertEquals([Match(start=4, end=7, dist=0)], matches) def test_missing_second_item(self): sequence = 'abcdefg' pattern = 'bde' matches = list(find_near_matches(pattern, sequence, max_l_dist=1)) self.assertIn(Match(start=1, end=5, dist=1), matches) #self.assertEquals([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(find_near_matches(pattern, text, max_l_dist=2)) self.assertTrue(len(matches) > 0) self.assertIn(Match(start=3, end=24, dist=1), matches) #self.assertEquals(1, len(matches)) class TestExpand(unittest.TestCase): def test_identical(self): self.assertEquals((0, 3), _expand('abc', 'abc', 0)) self.assertEquals((0, 3), _expand('abc', 'abc', 1)) self.assertEquals((0, 3), _expand('abc', 'abc', 2)) def test_one_missing(self): # first item missing self.assertEquals((1, 3), _expand('abcd', 'bcd', 1)) self.assertEquals((1, 3), _expand('abcd', 'bcd', 2)) # second item missing self.assertEquals((1, 3), _expand('abcd', 'acd', 1)) self.assertEquals((1, 3), _expand('abcd', 'acd', 2)) # last item missing self.assertEquals((1, 3), _expand('abcd', 'abc', 1)) self.assertEquals((1, 3), _expand('abcd', 'abc', 2)) def test_no_result(self): self.assertEquals((None, None), _expand('abc', 'def', 0)) def test_one_extra(self): self.assertEquals((1, 3), _expand('abcd', 'abd', 1)) self.assertEquals((1, 3), _expand('abcd', 'abd', 2)) class TestFuzzySearchBase(object): def search(self, subsequence, sequence, max_l_dist): raise NotImplementedError def test_empty_sequence(self): self.assertEquals([], 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.assertEquals( [Match(start=0, end=len('PATTERN'), dist=0)], self.search('PATTERN', 'PATTERN', max_l_dist=0), ) def test_substring(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTERNaaaaaaaaa' idx = text.find(substring) expected_match = Match(start=10, end=17, dist=0) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=0) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=1) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=2) ) def test_double_first_item(self): self.assertEquals( [Match(start=4, end=7, dist=0)], self.search('def', 'abcddefg', max_l_dist=1), ) def test_double_last_item(self): self.assertEquals( [Match(start=3, end=6, dist=0)], self.search('def', 'abcdeffg', max_l_dist=1), ) def test_double_first_items(self): self.assertEquals( [Match(start=5, end=10, dist=0)], self.search('defgh', 'abcdedefghi', max_l_dist=3), ) def test_double_last_items(self): self.assertEquals( [Match(start=2, end=8, dist=0)], self.search('cdefgh', 'abcdefghghi', max_l_dist=3), ) def test_missing_second_item(self): self.assertEquals( [Match(start=1, end=5, dist=1)], self.search('bde', 'abcdefg', max_l_dist=1), ) def test_missing_second_to_last_item(self): self.assertEquals( [Match(start=1, end=5, dist=1)], self.search('bce', 'abcdefg', max_l_dist=1), ) def test_one_missing_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATERNaaaaaaaaa' expected_match = Match(start=10, end=16, dist=1) self.assertEquals( [], self.search(substring, text, max_l_dist=0) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=1) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=2) ) def test_one_changed_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATtERNaaaaaaaaa' expected_match = Match(start=10, end=17, dist=1) self.assertEquals( [], self.search(substring, text, max_l_dist=0) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=1) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=2) ) def test_one_extra_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTXERNaaaaaaaaa' expected_match = Match(start=10, end=18, dist=1) self.assertEquals( [], self.search(substring, text, max_l_dist=0) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=1) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=2) ) def test_one_extra_repeating_in_middle(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTTERNaaaaaaaaa' expected_match = Match(start=10, end=18, dist=1) self.assertEquals( [], self.search(substring, text, max_l_dist=0) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=1) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=2) ) def test_one_extra_repeating_at_end(self): substring = 'PATTERN' text = 'aaaaaaaaaaPATTERNNaaaaaaaaa' expected_match = Match(start=10, end=17, dist=0) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=0) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=1) ) self.assertEquals( [expected_match], self.search(substring, text, max_l_dist=2) ) def test_one_missing_at_end_of_sequence(self): self.assertEquals( [Match(3, 6, 1)], self.search('defg', 'abcdef', max_l_dist=1) ) def test_dna_search(self): # see: http://stackoverflow.com/questions/19725127/ text = ''.join('''\ GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGT CACACACACATTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACAC ATTAGACGCGTACATAGACACAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATAC TCGCGTAGTCGTGGGAGGCAAGGCACACAGGGGATAGG '''.split()) pattern = 'TGCACTGTAGGGATAACAAT' self.assertEquals( [Match(start=3, end=24, dist=1)], self.search(pattern, text, max_l_dist=2), ) class TestFindNearMatchesWithNgrams(TestFuzzySearchBase, unittest.TestCase): def search(self, subsequence, sequence, max_l_dist): return find_near_matches_with_ngrams(subsequence, sequence, max_l_dist) class TestFindNearMatches(TestFuzzySearchBase, unittest.TestCase): def search(self, subsequence, sequence, max_l_dist): return [ get_best_match_in_group(group) for group in group_matches( find_near_matches(subsequence, sequence, max_l_dist) ) ]