def test_get_transitions(self):
seq = "AUGC"
alp = ["A", "U", "G", "C"]
out = [
[0.0, 1.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0]
]
self.assertEqual(prob.get_transitions(seq, alp, 1), out)
def __init__(self, seed, **kwargs):
self.seed = seed
alph = list(set(self.seed.target_seq))
self.__dict__.update({
'markov_order': 1,
'alphabet': alph,
'transitions': prob.get_transitions(self.seed.target_seq, alph, 1),
'motif_def': None,
'motif_upstream_extension': 0,
'motif_downstream_extension': 0,
'skip_exact': True,
})
self.__dict__.update(kwargs)
self._routine_done = False
def test_prob_motif(self):
seq = "AUGC"
alp = ["A", "U", "G", "C"]
t = prob.get_transitions(seq, alp, 1)
self.assertEqual(prob.prob_motif("AU", alp, 2, t), 1.0)
