Pomegranante library sample HMM code.

pomegranate_example.py

from pomegranate import *
d1 = DiscreteDistribution({'A' : 0.35, 'C' : 0.20, 'G' : 0.05, 'T' : 0.40})
d2 = DiscreteDistribution({'A' : 0.25, 'C' : 0.25, 'G' : 0.25, 'T' : 0.25})
d3 = DiscreteDistribution({'A' : 0.10, 'C' : 0.40, 'G' : 0.40, 'T' : 0.10})

s1 = State(d1, name="s1")
s2 = State(d2, name="s2")
s3 = State(d3, name="s3")

model = HiddenMarkovModel('example')
model.add_states([s1, s2, s3])
model.add_transition(model.start, s1, 0.90)
model.add_transition(model.start, s2, 0.10)
model.add_transition(s1, s1, 0.80)
model.add_transition(s1, s2, 0.20)
model.add_transition(s2, s2, 0.90)
model.add_transition(s2, s3, 0.10)
model.add_transition(s3, s3, 0.70)
model.add_transition(s3, model.end, 0.30)
model.bake()