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_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)
