def test_needleman_wunsch_sim_score(self):
"""Test abydos.distance.NeedlemanWunsch.sim_score."""
self.assertEqual(NeedlemanWunsch().sim_score('', ''), 0)
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm
self.assertEqual(
NeedlemanWunsch(1, _sim_nw).sim_score('GATTACA', 'GCATGCU'), 0
)
self.assertEqual(
NeedlemanWunsch(5, _sim_wikipedia).sim_score(
'AGACTAGTTAC', 'CGAGACGT'
),
16,
)
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=5, skew=5)
nw5 = NeedlemanWunsch(5, _sim_nw)
self.assertEqual(nw5.sim_score('CGATATCAG', 'TGACGSTGC'), -5)
self.assertEqual(nw5.sim_score('AGACTAGTTAC', 'TGACGSTGC'), -7)
self.assertEqual(nw5.sim_score('AGACTAGTTAC', 'CGAGACGT'), -15)
# test wrapper
self.assertEqual(
needleman_wunsch('AGACTAGTTAC', 'CGAGACGT', 5, _sim_nw), -15
)
def test_needleman_wunsch_dist_abs_nialls(self):
"""Test abydos.distance.NeedlemanWunsch.dist_abs (Nialls set)."""
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=2, skew=2)
nw_vals = (5, 0, -2, 3, 1, 1, -2, -2, -1, -3, -3, -5, -3, -7, -7, -19)
nw2 = NeedlemanWunsch(2, _sim_nw)
for i in range(len(NIALL)):
self.assertEqual(nw2.sim_score(NIALL[0], NIALL[i]), nw_vals[i])
def test_gotoh_sim_score_nialls(self):
"""Test abydos.distance.Gotoh.sim_score (Nialls set)."""
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=2, skew=2)
nw_vals = (5, 0, -2, 3, 1, 1, -2, -2, -1, -3, -3, -5, -3, -7, -7, -19)
g22 = Gotoh(2, 2, _sim_nw)
for i in range(len(NIALL)):
self.assertEqual(g22.sim_score(NIALL[0], NIALL[i]), nw_vals[i])
nw_vals2 = (5, 0, -2, 3, 1, 1, -2, -2, -1, -2, -3, -3, -2, -6, -6, -8)
g21 = Gotoh(2, 1, _sim_nw)
g205 = Gotoh(2, 0.5, _sim_nw)
nw2 = NeedlemanWunsch(2, _sim_nw)
for i in range(len(NIALL)):
self.assertEqual(g21.sim_score(NIALL[0], NIALL[i]), nw_vals2[i])
self.assertGreaterEqual(
g205.sim_score(NIALL[0], NIALL[i]),
nw2.sim_score(NIALL[0], NIALL[i]),
)
