def test_distance_pair(self):
"""get distances dict"""
calc = TN93Pair(DNA, alignment=self.alignment)
calc.run(show_progress=False)
dists = calc.get_pairwise_distances()
dists = dists.to_dict()
dist = 0.2554128119
expect = {("s1", "s2"): dist, ("s2", "s1"): dist}
self.assertEqual(list(dists.keys()), list(expect.keys()))
assert_allclose(list(dists.values()), list(expect.values()))
def test_tn93_from_matrix(self):
"""compute TN93 distances"""
calc = TN93Pair(DNA, alignment=self.alignment)
calc.run(show_progress=False)
self.assertEqual(calc.lengths["s1", "s2"], 10)
self.assertEqual(calc.proportions["s1", "s2"], 0.2)
# value from OSX MEGA 5
assert_allclose(calc.dists["s1", "s2"], 0.2554128119)
# value**2 from OSX MEGA 5
assert_allclose(calc.variances["s1", "s2"], 0.04444444445376601)
# value from OSX MEGA 5
assert_allclose(calc.stderr["s1", "s2"], 0.2108185107)
# same answer when using ambiguous alignment
calc.run(self.ambig_alignment, show_progress=False)
assert_allclose(calc.dists["s1", "s2"], 0.2554128119)
# but different answer if subsequent alignment is different
calc.run(self.diff_alignment, show_progress=False)
self.assertTrue(calc.dists["s1", "s2"] != 0.2554128119)
