def test_flatten(self):
i1 = range(2)
i2 = range(10, 12)
self.assertEqual(
utils.flatten([i1, i2]),
[0, 1, 10, 11]
)
def prob_motif(motif, alphabet, markov_order, transitions):
"""Computes the probability of a motif based on a transitions matrix"""
transitions = utils.flatten(transitions)
motifs = list(permutations(alphabet, markov_order+1))
motifs_index = dict([(motifs[i], i) for i in range(len(motifs))])
prob = 1.0
for i in range(len(motif) - markov_order):
prob *= transitions[motifs_index[motif[i:i+markov_order+1]]]
return prob
