def test_jc69_from_alignment(self):
"""compute JC69 dists from an alignment"""
calc = JC69Pair(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"], 0.2326161962)
# value**2 from OSX MEGA 5
assert_allclose(calc.variances["s1", "s2"], 0.029752066125078681)
# value from OSX MEGA 5
assert_allclose(calc.stderr["s1", "s2"], 0.1724878724)
# same answer when using ambiguous alignment
calc.run(self.ambig_alignment, show_progress=False)
assert_allclose(calc.dists["s1", "s2"], 0.2326161962)
# but different answer if subsequent alignment is different
calc.run(self.diff_alignment, show_progress=False)
self.assertTrue(calc.dists["s1", "s2"] != 0.2326161962)
def test_wrong_moltype(self):
"""specifying wrong moltype raises ValueError"""
with self.assertRaises(ValueError):
_ = JC69Pair(PROTEIN, alignment=self.alignment)