def test_hmmgraph(self):
"""Checking graphing process for HMM."""
obs_seq = 'AGACTGCATATATAAGGGGCAGGCTG'
sts_seq = '00000000111111100000000000'
a = hmm.HiddenMarkovModel().from_seq(obs_seq, sts_seq)
graph = a.graph_make()
self.assertTrue(isinstance(graph, Digraph))
def test_epm(self):
"""Checking emission probability matrix."""
result = np.array([[0.21052632, 0.21052632, 0.47368421, 0.10526316],
[0.57142857, 0., 0., 0.42857143]])
obs_seq = 'AGACTGCATATATAAGGGGCAGGCTG'
sts_seq = '00000000111111100000000000'
a = hmm.HiddenMarkovModel().from_seq(obs_seq, sts_seq)
self.assertTrue(np.allclose(a.ep, result))
def test_vit(self):
"""Checking Viterbi."""
obs_seq = 'AGACTGCATATATAAGGGGCAGGCTG'
sts_seq = '00000000111111100000000000'
a = hmm.HiddenMarkovModel().from_seq(obs_seq, sts_seq)
b = a.viterbi(obs_seq)
self.assertTrue(
isinstance(b[0], np.ndarray) and isinstance(b[1], np.ndarray))
def test_bw(self):
'''Checking Baum-Welch'''
obs_seq = 'AGACTGCATATATAAGGGGCAGGCTG'
sts_seq = '00000000111111100000000000'
a = hmm.HiddenMarkovModel().from_seq(obs_seq, sts_seq)
b = a.baum_welch(obs_seq, iters=3)
self.assertTrue(
isinstance(b[0], np.ndarray) and isinstance(b[1], np.ndarray))
def test_bw(self):
"""Checking Baum-Welch."""
obs_seq = 'AGACTGCATATATAAGGGGCAGGCTG'
a = hmm.HiddenMarkovModel().from_baum_welch(obs_seq, states=['0', '1'])
self.assertTrue(isinstance(a, hmm.HiddenMarkovModel))