def test_gtr(self):
f = [0.23, 0.31, 0.21]
s = sum(f)
f.append(1.0-s)
gtr = RevDiscreteModel(r_upper=[[1.0, 3.0, 1.2], [2.0, 4.1],[0.8]],
equil_freq=f)
m = gtr.get_probs(0.01)
assert_mat_eq(self, m, [[0.99204347826086958, 0.0019969565217391304, 0.0040317391304347822, 0.001926086956521739],
[0.0014816129032258064, 0.98928709677419346, 0.0026880645161290323, 0.0065419354838709672],
[0.0044157142857142858, 0.0039680952380952384, 0.9903238095238095, 0.0012942857142857144],
[0.0017719999999999999, 0.0081119999999999994, 0.0010872, 0.98902800000000002]])
def test_set_q_mat(self):
a = RevDiscreteModel(r_upper=[[1.0, 1.0, 1.0], [1.0, 1.0], [1.0],])
oth = 1.0/3.0
assert_list_eq(self, a.state_freqs, [0.25]*4)
assert_mat_eq(self, a.q_mat, [[-1.0, oth, oth, oth],
[oth, -1.0, oth, oth],
[oth, oth, -1.0, oth],
[oth, oth, oth, -1.0]])
a.r_upper = [[1.0, 2.0, 1.0], [1.0, 2.0], [1.0],] # kimura kappa=2
assert_list_eq(self, a.state_freqs, [0.25]*4)
assert_mat_eq(self, a.q_mat, [[-1.0, .25, .5, .25],
[.25, -1.0, .25, .5],
[.5, .25, -1.0, .25],
[.25, .5, .25, -1.0]])
a.state_freqs = [0.2, 0.3, 0.15, 0.35]
assert_list_eq(self, a.state_freqs, [0.2, 0.3, 0.15, 0.35])
exp = [[-0.9547738, 0.301507, 0.3015075, 0.351758],
[0.20100502, -1.05527638, 0.15075376, 0.7035175],
[0.40201005, 0.301507537, -1.05527638, 0.35175879],
[0.2010050, 0.603015075, 0.150753768, -0.954773869]]
assert_mat_eq(self, a.q_mat, exp)
