def get_transitions(seq, alphabet, markov_order):
"""Computes transitions matrix"""
transitions = []
motifs = list(permutations(alphabet, markov_order+1))
counts = dict(zip(motifs, [0]*len(motifs)))
for i in range(len(seq)-markov_order):
s = seq[i:i+markov_order+1]
if all([i in alphabet for i in s]):
counts[s] += 1
for motif in motifs:
transitions.append(counts[motif])
transitions = list(utils.grouper(len(alphabet), transitions))
sums = list(map(sum, transitions))
for i in range(len(transitions)):
if sums[i] != 0:
transitions[i] = [transitions[i][j] / float(sums[i]) for j in range(len(transitions[i]))]
else:
transitions[i] = [0.] * len(transitions[i])
return transitions
def test_grouper(self):
self.assertEqual(
list(utils.grouper(3, 'ABCDEFG', 'x')),
[('A', 'B', 'C'), ('D', 'E', 'F'), ('G', 'x', 'x')]
)
