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)
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)
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)