def _sim_wikipedia(src, tar):
"""Return a similarity score for two DNA base pairs.
Values copied from:
https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
int: similarity of two DNA base pairs
"""
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,
}
return NeedlemanWunsch.sim_matrix(
src, tar, nw_matrix, symmetric=True, alphabet='CGAT'
)
def _sim_wikipedia(src, tar):
"""Return a similarity score for two DNA base pairs.
Values copied from:
https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
int: similarity of two DNA base pairs
"""
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,
}
return NeedlemanWunsch.sim_matrix(
src, tar, nw_matrix, symmetric=True, alphabet='CGAT'
)
def test_sim_matrix(self):
"""Test abydos.distance.NeedlemanWunsch.sim_matrix."""
self.assertEqual(NeedlemanWunsch.sim_matrix('', ''), 1)
self.assertEqual(NeedlemanWunsch.sim_matrix('', 'a'), 0)
self.assertEqual(NeedlemanWunsch.sim_matrix('a', ''), 0)
self.assertEqual(NeedlemanWunsch.sim_matrix('a', 'a'), 1)
self.assertEqual(NeedlemanWunsch.sim_matrix('abcd', 'abcd'), 1)
self.assertEqual(NeedlemanWunsch.sim_matrix('abcd', 'dcba'), 0)
self.assertEqual(NeedlemanWunsch.sim_matrix('abc', 'cba'), 0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(_sim_wikipedia('A', 'C'), -3)
self.assertEqual(_sim_wikipedia('G', 'G'), 7)
self.assertEqual(_sim_wikipedia('A', 'A'), 10)
self.assertEqual(_sim_wikipedia('T', 'A'), -4)
self.assertEqual(_sim_wikipedia('T', 'C'), 0)
self.assertEqual(_sim_wikipedia('A', 'G'), -1)
self.assertEqual(_sim_wikipedia('C', 'T'), 0)
self.assertRaises(
ValueError, NeedlemanWunsch.sim_matrix, 'abc', 'cba', alphabet='ab'
)
self.assertRaises(
ValueError, NeedlemanWunsch.sim_matrix, 'abc', 'ba', alphabet='ab'
)
self.assertRaises(
ValueError, NeedlemanWunsch.sim_matrix, 'ab', 'cba', alphabet='ab'
)
def test_sim_matrix(self):
"""Test abydos.distance.NeedlemanWunsch.sim_matrix."""
self.assertEqual(NeedlemanWunsch.sim_matrix('', ''), 1)
self.assertEqual(NeedlemanWunsch.sim_matrix('', 'a'), 0)
self.assertEqual(NeedlemanWunsch.sim_matrix('a', ''), 0)
self.assertEqual(NeedlemanWunsch.sim_matrix('a', 'a'), 1)
self.assertEqual(NeedlemanWunsch.sim_matrix('abcd', 'abcd'), 1)
self.assertEqual(NeedlemanWunsch.sim_matrix('abcd', 'dcba'), 0)
self.assertEqual(NeedlemanWunsch.sim_matrix('abc', 'cba'), 0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(_sim_wikipedia('A', 'C'), -3)
self.assertEqual(_sim_wikipedia('G', 'G'), 7)
self.assertEqual(_sim_wikipedia('A', 'A'), 10)
self.assertEqual(_sim_wikipedia('T', 'A'), -4)
self.assertEqual(_sim_wikipedia('T', 'C'), 0)
self.assertEqual(_sim_wikipedia('A', 'G'), -1)
self.assertEqual(_sim_wikipedia('C', 'T'), 0)
self.assertRaises(
ValueError, NeedlemanWunsch.sim_matrix, 'abc', 'cba', alphabet='ab'
)
self.assertRaises(
ValueError, NeedlemanWunsch.sim_matrix, 'abc', 'ba', alphabet='ab'
)
self.assertRaises(
ValueError, NeedlemanWunsch.sim_matrix, 'ab', 'cba', alphabet='ab'
)