def test_smith_waterman_2(self):
seq1 = "a nice and short sentence to start with".split()
seq2 = "let's start with a really nice sentence".split()
scores, alignment = smith_waterman(seq1, seq2, self.sim_score, self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(6,1),(7,2)])
def test_needleman_wunsch_2(self):
seq1 = "SEND"
seq2 = "N"
scores, alignment = needleman_wunsch(seq1, seq2, self.sim_score, self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(2,0)])
def test_smith_waterman_1(self):
seq1 = "ABCCBA"
seq2 = "CBAABC"
scores, alignment = smith_waterman(seq1, seq2, self.sim_score, self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(3, 0), (4, 1), (5, 2)])
def test_smith_waterman_example(self):
seq1 = "CCAATCTACTACTGCTTGCAGTAC"
seq2 = "AGTCCGAGGGCTACTCTACTGAAC"
scores, alignment = smith_waterman(seq1, seq2, self.sim_score, self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(0, 10), (1, 11), (2, 12), (3, 13), (4,14),
(5, 15), (6, 16), (7, 17), (8, 18), (9, 19)])
def test_smith_waterman_2(self):
seq1 = "a nice and short sentence to start with".split()
seq2 = "let's start with a really nice sentence".split()
scores, alignment = smith_waterman(seq1, seq2, self.sim_score,
self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(6, 1), (7, 2)])
def test_smith_waterman_1(self):
seq1 = "ABCCBA"
seq2 = "CBAABC"
scores, alignment = smith_waterman(seq1, seq2, self.sim_score,
self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(3, 0), (4, 1), (5, 2)])
def test_needleman_wunsch_2(self):
seq1 = "SEND"
seq2 = "N"
scores, alignment = needleman_wunsch(seq1, seq2, self.sim_score,
self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment, [(2, 0)])
def test_smith_waterman_example(self):
seq1 = "CCAATCTACTACTGCTTGCAGTAC"
seq2 = "AGTCCGAGGGCTACTCTACTGAAC"
scores, alignment = smith_waterman(seq1, seq2, self.sim_score,
self.gap_cost)
print_scores(seq1, seq2, scores)
print_alignment(seq1, seq2, alignment)
self.assertEqual(alignment,
[(0, 10), (1, 11), (2, 12), (3, 13), (4, 14), (5, 15),
(6, 16), (7, 17), (8, 18), (9, 19)])