def test_smith_waterman_sim(self):
"""Test abydos.distance.SmithWaterman.sim."""
self.assertEqual(SmithWaterman().sim('', ''), 1.0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(
SmithWaterman(1, _sim_nw).sim('GATTACA', 'GCATGCU'), 0)
self.assertEqual(
SmithWaterman(5, _sim_wikipedia).sim('AGACTAGTTAC', 'CGAGACGT'),
0.3241905342349807,
)
sw5 = SmithWaterman(5, _sim_nw)
self.assertEqual(sw5.sim('CGATATCAG', 'TGACGSTGC'), 0)
self.assertEqual(sw5.sim('AGACTAGTTAC', 'TGACGSTGC'),
0.10050378152592121)
self.assertEqual(sw5.sim('AGACTAGTTAC', 'CGAGACGT'), 0)
def test_smith_waterman_sim_score(self):
"""Test abydos.distance.SmithWaterman.sim_score."""
self.assertEqual(SmithWaterman().sim_score('', ''), 0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(
SmithWaterman(1, _sim_nw).sim_score('GATTACA', 'GCATGCU'), 0)
self.assertEqual(
SmithWaterman(5, _sim_wikipedia).sim_score('AGACTAGTTAC',
'CGAGACGT'),
26,
)
sw5 = SmithWaterman(5, _sim_nw)
self.assertEqual(sw5.sim_score('CGATATCAG', 'TGACGSTGC'), 0)
self.assertEqual(sw5.sim_score('AGACTAGTTAC', 'TGACGSTGC'), 1)
self.assertEqual(sw5.sim_score('AGACTAGTTAC', 'CGAGACGT'), 0)
def test_smith_waterman_dist_abs(self):
"""Test abydos.distance.SmithWaterman.dist_abs."""
self.assertEqual(SmithWaterman().dist_abs('', ''), 0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(
SmithWaterman(1, _sim_nw).dist_abs('GATTACA', 'GCATGCU'), 0
)
self.assertEqual(
SmithWaterman(5, _sim_wikipedia).dist_abs(
'AGACTAGTTAC', 'CGAGACGT'
),
26,
)
sw5 = SmithWaterman(5, _sim_nw)
self.assertEqual(sw5.dist_abs('CGATATCAG', 'TGACGSTGC'), 0)
self.assertEqual(sw5.dist_abs('AGACTAGTTAC', 'TGACGSTGC'), 1)
self.assertEqual(sw5.dist_abs('AGACTAGTTAC', 'CGAGACGT'), 0)
# Test wrapper
self.assertEqual(
smith_waterman('AGACTAGTTAC', 'CGAGACGT', 5, _sim_wikipedia), 26
)
class SmithWatermanTestCases(unittest.TestCase):
"""Test Smith-Waterman functions.
abydos.distance.SmithWaterman
"""
cmp = SmithWaterman()
def test_smith_waterman_dist_abs(self):
"""Test abydos.distance.SmithWaterman.dist_abs."""
self.assertEqual(self.cmp.dist_abs('', ''), 0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(self.cmp.dist_abs('GATTACA', 'GCATGCU', 1, _sim_nw),
0)
self.assertEqual(
self.cmp.dist_abs('AGACTAGTTAC', 'CGAGACGT', 5, _sim_wikipedia),
26)
self.assertEqual(
self.cmp.dist_abs('CGATATCAG', 'TGACGSTGC', 5, _sim_nw), 0)
self.assertEqual(
self.cmp.dist_abs('AGACTAGTTAC', 'TGACGSTGC', 5, _sim_nw), 1)
self.assertEqual(
self.cmp.dist_abs('AGACTAGTTAC', 'CGAGACGT', 5, _sim_nw), 0)
# Test wrapper
self.assertEqual(
smith_waterman('AGACTAGTTAC', 'CGAGACGT', 5, _sim_wikipedia), 26)
def test_smith_waterman_dist_abs_nialls(self):
"""Test abydos.distance.SmithWaterman.dist_abs (Nialls set)."""
sw_vals = (5, 1, 1, 3, 2, 1, 1, 0, 0, 1, 1, 2, 2, 1, 0, 0)
for i in range(len(NIALL)):
self.assertEqual(self.cmp.dist_abs(NIALL[0], NIALL[i], 2, _sim_nw),
sw_vals[i])
def test_smith_waterman_sim_score_nialls(self):
"""Test abydos.distance.SmithWaterman.sim_score (Nialls set)."""
sw_vals = (5, 1, 1, 3, 2, 1, 1, 0, 0, 1, 1, 2, 2, 1, 0, 0)
sw2 = SmithWaterman(2, _sim_nw)
for i in range(len(NIALL)):
self.assertEqual(sw2.sim_score(NIALL[0], NIALL[i]), sw_vals[i])
def test_smith_waterman_dist_abs_nialls(self):
"""Test abydos.distance.SmithWaterman.dist_abs (Nialls set)."""
sw_vals = (5, 1, 1, 3, 2, 1, 1, 0, 0, 1, 1, 2, 2, 1, 0, 0)
sw2 = SmithWaterman(2, _sim_nw)
for i in range(len(NIALL)):
self.assertEqual(sw2.dist_abs(NIALL[0], NIALL[i]), sw_vals[i])