def test_paralinear_continuous_time(self):
"""paralinear_continuous_time is additive from random matrices"""
qp1, qp2, qp3 = gen_qs_ps()
pi1 = random(4)
pi1 /= pi1.sum()
pi2 = next_pi(pi1, qp1[1])
pl1 = paralinear_continuous_time(qp1[1], pi1, qp1[0])
pl2 = paralinear_continuous_time(qp2[1], pi2, qp2[0])
pl3 = paralinear_continuous_time(qp3[1], pi1, qp3[0])
assert_allclose(pl1 + pl2, pl3)
def get_paralinear_metric(self, motif_probs=None):
"""returns {edge.name: paralinear, ...}
Parameters
----------
motif_probs : dict or DictArray
an item for each edge of the tree. Computed if not provided.
"""
from cogent3.evolve.ns_substitution_model import DiscreteSubstitutionModel
is_discrete = isinstance(self.model, DiscreteSubstitutionModel)
if motif_probs is None:
motif_probs = self.get_motif_probs_by_node()
plin = {}
for edge in self.tree.get_edge_vector(include_root=False):
parent_name = edge.parent.name
pi = motif_probs[parent_name]
P = self.get_psub_for_edge(edge.name)
if is_discrete:
para = paralinear_discrete_time(P.array, pi.array)
else:
Q = self.get_rate_matrix_for_edge(edge.name, calibrated=False)
para = paralinear_continuous_time(P.array, pi.array, Q.array)
plin[edge.name] = para
return plin
def test_paralinear_discrete_time(self):
"""tests paralinear_discrete_time to compare it with the output of paralinear_continuous_time"""
qp1, qp2, qp3 = gen_qs_ps()
pi1 = random(4)
pi1 /= pi1.sum()
pi2 = next_pi(pi1, qp1[1])
pi3 = next_pi(pi2, qp2[1])
con_time_pl1 = paralinear_continuous_time(qp1[1], pi1, qp1[0])
dis_time_pl1 = paralinear_discrete_time(qp1[1], pi1)
assert_allclose(con_time_pl1, dis_time_pl1)
con_time_pl2 = paralinear_continuous_time(qp2[1], pi2, qp2[0])
dis_time_pl2 = paralinear_discrete_time(qp2[1], pi2)
assert_allclose(con_time_pl2, dis_time_pl2)
con_time_pl3 = paralinear_continuous_time(qp3[1], pi3, qp3[0])
dis_time_pl3 = paralinear_discrete_time(qp3[1], pi3)
assert_allclose(con_time_pl3, dis_time_pl3)
def test_paralinear_continuous_time_validate(self):
"""paralinear_continuous_time validate check consistency"""
qp1, qp2, qp3 = gen_qs_ps()
pi1 = random(4)
with self.assertRaises(AssertionError):
paralinear_continuous_time(
qp1[1], qp1[0], qp1[0], validate=True
) # pi invalid shape
with self.assertRaises(AssertionError):
paralinear_continuous_time(
qp1[1], pi1, qp1[0], validate=True
) # pi invalid values
pi1 /= pi1.sum()
with self.assertRaises(AssertionError):
paralinear_continuous_time(qp1[1], pi1, qp1[1], validate=True) # invalid Q
with self.assertRaises(AssertionError):
paralinear_continuous_time(qp1[0], pi1, qp1[0], validate=True) # invalid P
qp2[0][0, 0] = 9
with self.assertRaises(AssertionError):
paralinear_continuous_time(qp1[1], pi1, qp2[0], validate=True) # invalid Q
qp2[1][0, 3] = 9
with self.assertRaises(AssertionError):
paralinear_continuous_time(qp2[1], pi1, qp1[0], validate=True) # invalid P
