def test_toRates(self):
"""Probs toRates should return log of probs, optionally normalized"""
a = Alphabet('abc')**2
p = Probs([0.9,0.05,0.05,0.1,0.85,0.05,0.02,0.02,0.96], a)
assert p.isValid()
r = p.toRates()
assert isinstance(r, Rates)
assert r.isValid()
assert not r.isComplex()
self.assertEqual(r._data, logm(p._data))
r_norm = p.toRates(normalize=True)
self.assertFloatEqual(trace(r_norm._data), -1.0)
def test_toRates(self):
"""Probs toRates should return log of probs, optionally normalized"""
a = Alphabet('abc')**2
p = Probs([0.9, 0.05, 0.05, 0.1, 0.85, 0.05, 0.02, 0.02, 0.96], a)
assert p.isValid()
r = p.toRates()
assert isinstance(r, Rates)
assert r.isValid()
assert not r.isComplex()
self.assertEqual(r._data, logm(p._data))
r_norm = p.toRates(normalize=True)
self.assertFloatEqual(trace(r_norm._data), -1.0)
def test_timeForSimilarity(self):
"""Rates timeToSimilarity should return correct time"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.15, 0.8], a)
q = p.toRates()
d = 0.5
t = q.timeForSimilarity(d)
x = expm(q._data)(t)
self.assertFloatEqual(average(diagonal(x), axis=0), d)
t = q.timeForSimilarity(d, array([1/3.0]*3))
x = expm(q._data)(t)
self.assertFloatEqual(average(diagonal(x), axis=0), d)
self.assertEqual(q.timeForSimilarity(1), 0)
def test_timeForSimilarity(self):
"""Rates timeToSimilarity should return correct time"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.15, 0.8], a)
q = p.toRates()
d = 0.5
t = q.timeForSimilarity(d)
x = expm(q._data)(t)
self.assertFloatEqual(average(diagonal(x), axis=0), d)
t = q.timeForSimilarity(d, array([1 / 3.0] * 3))
x = expm(q._data)(t)
self.assertFloatEqual(average(diagonal(x), axis=0), d)
self.assertEqual(q.timeForSimilarity(1), 0)
def test_toSimilarProbs(self):
"""Rates toSimilarProbs should match individual steps"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.15, 0.8], a)
q = p.toRates()
self.assertEqual(q.toSimilarProbs(0.5), \
q.toProbs(q.timeForSimilarity(0.5)))
#test a case that didn't work for DNA
q = Rates(array(
[[-0.64098451, 0.0217681 , 0.35576469, 0.26345171],
[ 0.31144238, -0.90915091, 0.25825858, 0.33944995],
[ 0.01578521, 0.43162879, -0.99257581, 0.54516182],
[ 0.13229986, 0.04027147, 0.05817791, -0.23074925]]),
DnaPairs)
p = q.toSimilarProbs(0.66)
self.assertFloatEqual(average(diagonal(p._data), axis=0), 0.66)
def test_toProbs(self):
"""Rates toProbs should return correct probability matrix"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.1, 0.85], a)
q = p.toRates()
self.assertEqual(q._data, logm(p._data))
p2 = q.toProbs()
self.assertFloatEqual(p2._data, p._data)
#test a case that didn't work for DNA
q = Rates(array(
[[-0.64098451, 0.0217681 , 0.35576469, 0.26345171],
[ 0.31144238, -0.90915091, 0.25825858, 0.33944995],
[ 0.01578521, 0.43162879, -0.99257581, 0.54516182],
[ 0.13229986, 0.04027147, 0.05817791, -0.23074925]]),
DnaPairs)
self.assertFloatEqual(q.toProbs(0.5)._data, expm(q._data)(t=0.5))
def test_toSimilarProbs(self):
"""Rates toSimilarProbs should match individual steps"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.15, 0.8], a)
q = p.toRates()
self.assertEqual(q.toSimilarProbs(0.5), \
q.toProbs(q.timeForSimilarity(0.5)))
#test a case that didn't work for DNA
q = Rates(
array([[-0.64098451, 0.0217681, 0.35576469, 0.26345171],
[0.31144238, -0.90915091, 0.25825858, 0.33944995],
[0.01578521, 0.43162879, -0.99257581, 0.54516182],
[0.13229986, 0.04027147, 0.05817791, -0.23074925]]),
DnaPairs)
p = q.toSimilarProbs(0.66)
self.assertFloatEqual(average(diagonal(p._data), axis=0), 0.66)
def test_toProbs(self):
"""Rates toProbs should return correct probability matrix"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.1, 0.85], a)
q = p.toRates()
self.assertEqual(q._data, logm(p._data))
p2 = q.toProbs()
self.assertFloatEqual(p2._data, p._data)
#test a case that didn't work for DNA
q = Rates(
array([[-0.64098451, 0.0217681, 0.35576469, 0.26345171],
[0.31144238, -0.90915091, 0.25825858, 0.33944995],
[0.01578521, 0.43162879, -0.99257581, 0.54516182],
[0.13229986, 0.04027147, 0.05817791, -0.23074925]]),
DnaPairs)
self.assertFloatEqual(q.toProbs(0.5)._data, expm(q._data)(t=0.5))