def test_common(self):
# https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
nw_matrix = {
('A', 'A'): 10,
('G', 'G'): 7,
('C', 'C'): 9,
('T', 'T'): 8,
('A', 'G'): -1,
('A', 'C'): -3,
('A', 'T'): -4,
('G', 'C'): -5,
('G', 'T'): -3,
('C', 'T'): 0,
}
sim_matrix = textdistance.Matrix(nw_matrix, symmetric=True)
alg = self.alg(sim_func=sim_matrix)
# self.assertEqual(alg('AGACTAGTTAC', 'CGAGACGT'), 26)
alg = self.alg(gap_open=1, gap_ext=1, sim_func=sim_ident)
self.assertEqual(alg('GATTACA', 'GCATGCU'), 0)
alg = self.alg(gap_open=1, gap_ext=.5, sim_func=sim_ident)
self.assertEqual(alg('GATTACA', 'GCATGCU'), 0)
self.assertEqual(alg('AGACTAGTTAC', 'TGACGSTGC'), 1.5)
self.assertEqual(alg('AGACTAGTTAC', 'CGAGACGT'), 1)
alg = self.alg(gap_open=5, gap_ext=5, sim_func=sim_ident)
self.assertEqual(alg('AGACTAGTTAC', 'CGAGACGT'), -15)
def test_common(self):
# https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
nw_matrix = {
('A', 'A'): 10,
('G', 'G'): 7,
('C', 'C'): 9,
('T', 'T'): 8,
('A', 'G'): -1,
('A', 'C'): -3,
('A', 'T'): -4,
('G', 'C'): -5,
('G', 'T'): -3,
('C', 'T'): 0,
}
alg = textdistance.Matrix(nw_matrix, symmetric=True)
self.assertEqual(alg('', ''), 1)
self.assertEqual(alg('', 'a'), 0)
self.assertEqual(alg('abcd', 'abcd'), 1)
self.assertEqual(alg('A', 'C'), -3)
self.assertEqual(alg('G', 'G'), 7)
self.assertEqual(alg('A', 'A'), 10)
self.assertEqual(alg('T', 'A'), -4)
self.assertEqual(alg('T', 'C'), 0)
self.assertEqual(alg('A', 'G'), -1)
self.assertEqual(alg('C', 'T'), 0)
def test_common(self):
# https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
nw_matrix = {
('A', 'A'): 10,
('G', 'G'): 7,
('C', 'C'): 9,
('T', 'T'): 8,
('A', 'G'): -1,
('A', 'C'): -3,
('A', 'T'): -4,
('G', 'C'): -5,
('G', 'T'): -3,
('C', 'T'): 0,
}
sim_matrix = textdistance.Matrix(nw_matrix, symmetric=True)
alg = self.alg(gap_cost=5, sim_func=sim_matrix)
self.assertEqual(alg('AGACTAGTTAC', 'CGAGACGT'), 26)
sim_ident = lambda x, y: 2 * int(x == y) - 1
alg = self.alg(sim_func=sim_ident)
self.assertEqual(alg('GATTACA', 'GCATGCU'), 0)
alg = self.alg(gap_cost=5, sim_func=sim_ident)
self.assertEqual(alg('CGATATCAG', 'TGACGSTGC'), 0)
self.assertEqual(alg('AGACTAGTTAC', 'TGACGSTGC'), 1)
self.assertEqual(alg('AGACTAGTTAC', 'CGAGACGT'), 0)