def test_mean(self):
rhtype = RateHetType.GAMMA_EQ_CAT_MEAN
rhm = RateHetManager(shape=0.5, num_categories=4, rate_het_type=rhtype)
expected = [0.03338775, 0.25191592, 0.82026848, 2.89442785]
assert_list_eq(self, rhm.rates, expected)
self.assertEqual(rhm.num_categories, 4)
self.assertTrue(abs(rhm.shape - 0.5) < 1.0e-5)
rhm.set_shape(4.2)
expected = [0.46502269, 0.78185321, 1.08432009, 1.66880400]
assert_list_eq(self, rhm.rates, expected)
self.assertEqual(rhm.num_categories, 4)
self.assertEqual(rhm.shape, 4.2)
self.assertTrue(abs(rhm.shape - 4.2) < 1.0e-5)
rhm = RateHetManager(shape=0.53, num_categories=10, rate_het_type=rhtype)
expected = [
0.00680095,
0.04407109,
0.11615143,
0.22625412,
0.38203227,
0.59769745,
0.90010946,
1.34639481,
2.09367223,
4.28681618,
]
assert_list_eq(self, rhm.rates, expected)
self.assertEqual(rhm.num_categories, 10)
self.assertTrue(abs(rhm.shape - 0.53) < 1.0e-5)
def test_median(self):
rhtype = RateHetType.GAMMA_EQ_CAT_MEDIAN
rhm = RateHetManager(shape=0.5, num_categories=4, rate_het_type=rhtype)
expected = [0.02907775, 0.28071453, 0.92477307, 2.76543465]
assert_list_eq(self, rhm.rates, expected)
rhm.set_shape(4.2)
expected = [0.49655820, 0.79929783, 1.10263121, 1.60151276]
assert_list_eq(self, rhm.rates, expected)
def test_hashing(self):
rhm = RateHetManager(shape=0.5, num_categories=4, rate_het_type=RateHetType.GAMMA_EQ_CAT_MEAN)
h1 = rhm.state_hash
rhm.shape = 0.6
h2 = rhm.state_hash
self.assertNotEqual(h1, h2)