Example #1
0
 def test_waterman_eggert_2(self):
     seq1 = "a nice and short sentence to start with".split()
     seq2 = "let's start with a really nice sentence".split()
     all_scores, all_alignments = waterman_eggert(seq1, seq2,
                                                  self.sim_score,
                                                  self.gap_cost)
     print_all_scores_and_alignments(seq1, seq2, all_scores, all_alignments)
     result = [[(6, 1), (7, 2)], [(0, 3)], [(1, 4)], [(1, 5)], [(2, 6)],
               [(4, 6)]]
     self.assertEqual(all_alignments, result)
 def test_waterman_eggert_2(self):
     seq1 = "a nice and short sentence to start with".split()
     seq2 = "let's start with a really nice sentence".split()
     all_scores, all_alignments = waterman_eggert(seq1, seq2, self.sim_score, self.gap_cost)
     print_all_scores_and_alignments(seq1, seq2, all_scores, all_alignments)
     result = [[(6, 1), (7, 2)], 
               [(0, 3)], 
               [(1, 4)], 
               [(1, 5)], 
               [(2, 6)], 
               [(4, 6)]]
     self.assertEqual(all_alignments, result)
 def test_waterman_eggert_example(self):
     seq1 = "CCAATCTACTACTGCTTGCAGTAC"
     seq2 = "AGTCCGAGGGCTACTCTACTGAAC"
     all_scores, all_alignments = waterman_eggert(seq1, seq2, self.sim_score, self.gap_cost,
                                                  limit=3)
     print_all_scores_and_alignments(seq1, seq2, all_scores, all_alignments)
     result = [[(0, 10), (1, 11), (2, 12), (3, 13), (4, 14), (5, 15), (6, 16), (7, 17), 
                (8, 18), (9, 19)], 
                [(5, 10), (6, 11), (7, 12), (8, 13), (9, 14), (11, 15), (12, 16), 
                 (13, 17), (14, 18), (15, 19)], 
                [(8, 15), (9, 16), (10, 17), (11, 18), (12, 19), (13, 20)] ]
     self.assertEqual(all_alignments, result)
Example #4
0
 def test_waterman_eggert_1(self):
     seq1 = "ABCCBA"
     seq2 = "CBAABC"
     all_scores, all_alignments = waterman_eggert(seq1, seq2,
                                                  self.sim_score,
                                                  self.gap_cost)
     print_all_scores_and_alignments(seq1, seq2, all_scores, all_alignments)
     result = [[(0, 3), (1, 4), (2, 5)], [(3, 0), (4, 1), (5, 2)],
               [(0, 2), (1, 3), (2, 4), (3, 5)], [(0, 3), (1, 4), (2, 5)],
               [(1, 1), (2, 2), (3, 3), (4, 4)],
               [(2, 0), (3, 1), (4, 2), (5, 3)], [(3, 0), (4, 1), (5, 2)],
               [(3, 5)], [(5, 3)]]
     self.assertEqual(all_alignments, result)
 def test_waterman_eggert_1(self):
     seq1 = "ABCCBA"
     seq2 = "CBAABC"
     all_scores, all_alignments = waterman_eggert(seq1, seq2, self.sim_score, self.gap_cost)
     print_all_scores_and_alignments(seq1, seq2, all_scores, all_alignments)
     result = [[(0, 3), (1, 4), (2, 5)], 
               [(3, 0), (4, 1), (5, 2)], 
               [(0, 2), (1, 3), (2, 4), (3, 5)], 
               [(0, 3), (1, 4), (2, 5)], 
               [(1, 1), (2, 2), (3, 3), (4, 4)], 
               [(2, 0), (3, 1), (4, 2), (5, 3)], 
               [(3, 0), (4, 1), (5, 2)], 
               [(3, 5)], [(5, 3)] ]
     self.assertEqual(all_alignments, result)
Example #6
0
 def test_waterman_eggert_example(self):
     seq1 = "CCAATCTACTACTGCTTGCAGTAC"
     seq2 = "AGTCCGAGGGCTACTCTACTGAAC"
     all_scores, all_alignments = waterman_eggert(seq1,
                                                  seq2,
                                                  self.sim_score,
                                                  self.gap_cost,
                                                  limit=3)
     print_all_scores_and_alignments(seq1, seq2, all_scores, all_alignments)
     result = [[(0, 10), (1, 11), (2, 12), (3, 13), (4, 14), (5, 15),
                (6, 16), (7, 17), (8, 18), (9, 19)],
               [(5, 10), (6, 11), (7, 12), (8, 13), (9, 14), (11, 15),
                (12, 16), (13, 17), (14, 18), (15, 19)],
               [(8, 15), (9, 16), (10, 17), (11, 18), (12, 19), (13, 20)]]
     self.assertEqual(all_alignments, result)