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test_MarkovModel.py
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test_MarkovModel.py
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# Copyright 2002 by Jeffrey Chang. All rights reserved.
# Revisions copyright 2008 by Brad Chapman. All rights reserved.
# Revisions copyright 2008 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2008-2010,2013-2014 by Peter Cock. All rights reserved.
# Revisions copyright 2012 by Christian Brueffer. All rights reserved.
# Revisions copyright 2017 by Maximilian Greil. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Tests for MarkovModel module."""
import warnings
import unittest
from io import StringIO
try:
from numpy import array
from numpy import random # missing in PyPy's micronumpy
from numpy import array_equal
from numpy import around
from numpy import log
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.MarkovModel.") from None
with warnings.catch_warnings():
# Silence this warning:
# For optimal speed, please update to Numpy version 1.3 or later
warnings.simplefilter("ignore", UserWarning)
from Bio import MarkovModel
class TestMarkovModel(unittest.TestCase):
def test_train_visible(self):
states = ["0", "1", "2", "3"]
alphabet = ["A", "C", "G", "T"]
training_data = [
("AACCCGGGTTTTTTT", "001112223333333"),
("ACCGTTTTTTT", "01123333333"),
("ACGGGTTTTTT", "01222333333"),
("ACCGTTTTTTTT", "011233333333"),
]
markov_model = MarkovModel.train_visible(states, alphabet, training_data)
states = MarkovModel.find_states(markov_model, "AACGTT")
self.assertEqual(len(states), 1)
state_list, state_float = states[0]
self.assertEqual(state_list, ["0", "0", "1", "2", "3", "3"])
self.assertAlmostEqual(state_float, 0.0082128906)
self.assertEqual(markov_model.states, ["0", "1", "2", "3"])
self.assertEqual(markov_model.alphabet, ["A", "C", "G", "T"])
self.assertEqual(len(markov_model.p_initial), 4)
self.assertAlmostEqual(markov_model.p_initial[0], 1.0)
self.assertAlmostEqual(markov_model.p_initial[1], 0.0)
self.assertAlmostEqual(markov_model.p_initial[2], 0.0)
self.assertAlmostEqual(markov_model.p_initial[3], 0.0)
self.assertEqual(len(markov_model.p_transition), 4)
self.assertEqual(len(markov_model.p_transition[0]), 4)
self.assertEqual(len(markov_model.p_transition[1]), 4)
self.assertEqual(len(markov_model.p_transition[2]), 4)
self.assertEqual(len(markov_model.p_transition[3]), 4)
self.assertAlmostEqual(markov_model.p_transition[0][0], 0.2)
self.assertAlmostEqual(markov_model.p_transition[0][1], 0.8)
self.assertAlmostEqual(markov_model.p_transition[0][2], 0.0)
self.assertAlmostEqual(markov_model.p_transition[0][3], 0.0)
self.assertAlmostEqual(markov_model.p_transition[1][0], 0.0)
self.assertAlmostEqual(markov_model.p_transition[1][1], 0.5)
self.assertAlmostEqual(markov_model.p_transition[1][2], 0.5)
self.assertAlmostEqual(markov_model.p_transition[1][3], 0.0)
self.assertAlmostEqual(markov_model.p_transition[2][0], 0.0)
self.assertAlmostEqual(markov_model.p_transition[2][1], 0.0)
self.assertAlmostEqual(markov_model.p_transition[2][2], 0.5)
self.assertAlmostEqual(markov_model.p_transition[2][3], 0.5)
self.assertAlmostEqual(markov_model.p_transition[3][0], 0.0)
self.assertAlmostEqual(markov_model.p_transition[3][1], 0.0)
self.assertAlmostEqual(markov_model.p_transition[3][2], 0.0)
self.assertAlmostEqual(markov_model.p_transition[3][3], 1.0)
self.assertEqual(len(markov_model.p_emission), 4)
self.assertEqual(len(markov_model.p_emission[0]), 4)
self.assertEqual(len(markov_model.p_emission[1]), 4)
self.assertEqual(len(markov_model.p_emission[2]), 4)
self.assertEqual(len(markov_model.p_emission[3]), 4)
self.assertAlmostEqual(markov_model.p_emission[0][0], 0.666667,
places=4)
self.assertAlmostEqual(markov_model.p_emission[0][1], 0.111111,
places=4)
self.assertAlmostEqual(markov_model.p_emission[0][2], 0.111111,
places=4)
self.assertAlmostEqual(markov_model.p_emission[0][3], 0.111111,
places=4)
self.assertAlmostEqual(markov_model.p_emission[1][0], 0.083333,
places=4)
self.assertAlmostEqual(markov_model.p_emission[1][1], 0.750000,
places=4)
self.assertAlmostEqual(markov_model.p_emission[1][2], 0.083333,
places=4)
self.assertAlmostEqual(markov_model.p_emission[1][3], 0.083333,
places=4)
self.assertAlmostEqual(markov_model.p_emission[2][0], 0.083333,
places=4)
self.assertAlmostEqual(markov_model.p_emission[2][1], 0.083333,
places=4)
self.assertAlmostEqual(markov_model.p_emission[2][2], 0.750000,
places=4)
self.assertAlmostEqual(markov_model.p_emission[2][3], 0.083333,
places=4)
self.assertAlmostEqual(markov_model.p_emission[3][0], 0.031250,
places=4)
self.assertAlmostEqual(markov_model.p_emission[3][1], 0.031250,
places=4)
self.assertAlmostEqual(markov_model.p_emission[3][2], 0.031250,
places=4)
self.assertAlmostEqual(markov_model.p_emission[3][3], 0.906250,
places=4)
def test_baum_welch(self):
states = ["CP", "IP"]
alphabet = ["cola", "ice_t", "lem"]
outputs = [
(2, 1, 0)
]
p_initial = [1.0, 0.0000001]
p_transition = [[0.7, 0.3],
[0.5, 0.5]]
p_emission = [[0.6, 0.1, 0.3],
[0.1, 0.7, 0.2]]
N, M = len(states), len(alphabet)
x = MarkovModel._baum_welch(N, M, outputs,
p_initial=p_initial,
p_transition=p_transition,
p_emission=p_emission
)
p_initial, p_transition, p_emission = x
markov_model = MarkovModel.MarkovModel(states, alphabet,
p_initial, p_transition,
p_emission)
self.assertEqual(markov_model.states, ["CP", "IP"])
self.assertEqual(markov_model.alphabet, ["cola", "ice_t", "lem"])
self.assertEqual(len(markov_model.p_initial), 2)
self.assertAlmostEqual(markov_model.p_initial[0], 1.0,
places=4)
self.assertAlmostEqual(markov_model.p_initial[1], 0.0,
places=4)
self.assertEqual(len(markov_model.p_transition), 2)
self.assertEqual(len(markov_model.p_transition[0]), 2)
self.assertEqual(len(markov_model.p_transition[1]), 2)
self.assertAlmostEqual(markov_model.p_transition[0][0], 0.02460365,
places=4)
self.assertAlmostEqual(markov_model.p_transition[0][1], 0.97539634,
places=4)
self.assertAlmostEqual(markov_model.p_transition[1][0], 1.0,
places=4)
self.assertAlmostEqual(markov_model.p_transition[1][1], 0.0,
places=4)
self.assertEqual(len(markov_model.p_emission), 2)
self.assertEqual(len(markov_model.p_emission[0]), 3)
self.assertEqual(len(markov_model.p_emission[1]), 3)
self.assertAlmostEqual(markov_model.p_emission[0][0], 0.5)
self.assertAlmostEqual(markov_model.p_emission[0][1], 0.0)
self.assertAlmostEqual(markov_model.p_emission[0][2], 0.5)
self.assertAlmostEqual(markov_model.p_emission[1][0], 0.0)
self.assertAlmostEqual(markov_model.p_emission[1][1], 1.0)
self.assertAlmostEqual(markov_model.p_emission[1][2], 0.0)
# Do some tests from the topcoder competition.
def test_topcoder1(self):
# NNNN
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.90, 0.10],
[0.20, 0.80]])
p_emission = array([[0.30, 0.20, 0.30, 0.20],
[0.10, 0.40, 0.10, 0.40]])
markov_model = MarkovModel.MarkovModel(
states, alphabet, p_initial, p_transition, p_emission)
states = MarkovModel.find_states(markov_model, "TGCC")
self.assertEqual(len(states), 1)
state_list, state_float = states[0]
self.assertEqual(state_list, ["N", "N", "N", "N"])
def test_topcoder2(self):
# NNNRRRNNRRNRRN
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.56, 0.44],
[0.25, 0.75]])
p_emission = array([[0.04, 0.14, 0.62, 0.20],
[0.39, 0.15, 0.04, 0.42]])
markov_model = MarkovModel.MarkovModel(
states, alphabet, p_initial, p_transition, p_emission)
states = MarkovModel.find_states(markov_model, "CCTGAGTTAGTCGT")
self.assertEqual(len(states), 1)
state_list, state_float = states[0]
self.assertEqual(state_list, ["N", "N", "N", "R", "R", "R", "N", "N", "R", "R", "N", "R", "R", "N"])
def test_topcoder3(self):
# NRRRRRRRRRRRNNNNRRRRRRRRR
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.75, 0.25],
[0.25, 0.75]])
p_emission = array([[0.45, 0.36, 0.06, 0.13],
[0.24, 0.18, 0.12, 0.46]])
markov_model = MarkovModel.MarkovModel(
states, alphabet, p_initial, p_transition, p_emission)
states = MarkovModel.find_states(markov_model, "CCGTACTTACCCAGGACCGCAGTCC")
self.assertEqual(len(states), 1)
state_list, state_float = states[0]
self.assertEqual(state_list, ["N", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "N", "N", "N", "N", "R", "R", "R", "R", "R", "R", "R", "R", "R"])
def test_topcoder4(self):
# NRRRRRRRRRR
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.55, 0.45],
[0.15, 0.85]])
p_emission = array([[0.75, 0.03, 0.01, 0.21],
[0.34, 0.11, 0.39, 0.16]])
markov_model = MarkovModel.MarkovModel(
states, alphabet, p_initial, p_transition, p_emission)
states = MarkovModel.find_states(markov_model, "TTAGCAGTGCG")
self.assertEqual(len(states), 1)
state_list, state_float = states[0]
self.assertEqual(state_list, ["N", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R"])
def test_topcoder5(self):
# N
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.84, 0.16],
[0.25, 0.75]])
p_emission = array([[0.26, 0.37, 0.08, 0.29],
[0.31, 0.13, 0.33, 0.23]])
markov_model = MarkovModel.MarkovModel(
states, alphabet, p_initial, p_transition, p_emission)
states = MarkovModel.find_states(markov_model, "T")
self.assertEqual(len(states), 1)
state_list, state_float = states[0]
self.assertEqual(state_list, ["N"])
def test_readline_and_check_start(self):
states = "NR"
alphabet = "AGTC"
markov_model = MarkovModel.MarkovModel(states, alphabet)
line = "This is a \n string with two lines \n"
handle = StringIO(line)
start = "This is a \n"
self.assertEqual(
start, MarkovModel._readline_and_check_start(handle, start))
def test_save_and_load(self):
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.75, 0.25], [0.25, 0.75]])
p_emission = array(
[[0.45, 0.36, 0.06, 0.13], [0.24, 0.18, 0.12, 0.46]])
markov_model_save = MarkovModel.MarkovModel(
states,
alphabet,
p_initial,
p_transition,
p_emission)
handle = StringIO()
MarkovModel.save(markov_model_save, handle)
handle.seek(0)
markov_model_load = MarkovModel.load(handle)
self.assertEqual("".join(markov_model_load.states), states)
self.assertEqual("".join(markov_model_load.alphabet), alphabet)
self.assertTrue(array_equal(markov_model_load.p_initial, p_initial))
self.assertTrue(array_equal
(markov_model_load.p_transition, p_transition))
self.assertTrue(array_equal(markov_model_load.p_emission, p_emission))
def test_train_bw(self):
random.seed(0)
states = ["0", "1", "2", "3"]
alphabet = ["A", "C", "G", "T"]
training_data = ["AACCCGGGTTTTTTT", "ACCGTTTTTTT",
"ACGGGTTTTTT", "ACCGTTTTTTTT"]
output_p_initial = array([0.2275677, 0.29655611,
0.24993822, 0.22593797])
output_p_transition = array(
[[5.16919807e-001, 3.65825814e-033, 4.83080193e-001, 9.23220689e-042],
[3.65130247e-001,
1.00000000e-300,
6.34869753e-001,
1.00000000e-300],
[8.68776164e-001,
1.02254304e-034,
1.31223836e-001,
6.21835051e-047],
[3.33333333e-301, 3.33333333e-001, 3.33333333e-301, 6.66666667e-001]])
output_p_emission = array(
[[2.02593570e-301, 2.02593570e-301, 2.02593570e-301, 1.00000000e+000],
[1.00000000e-300,
1.00000000e-300,
1.00000000e+000,
1.09629016e-259],
[3.26369779e-301,
3.26369779e-301,
3.26369779e-301,
1.00000000e+000],
[3.33333333e-001, 6.66666667e-001, 3.33333333e-301, 3.33333333e-301]])
markov_model = MarkovModel.train_bw(states, alphabet, training_data)
self.assertEqual("".join(markov_model.states), "".join(states))
self.assertEqual("".join(markov_model.alphabet), "".join(alphabet))
self.assertTrue(array_equal(
around(markov_model.p_initial, decimals=3),
around(output_p_initial, decimals=3)))
self.assertTrue(array_equal(around(
markov_model.p_transition, decimals=3),
around(output_p_transition, decimals=3)))
self.assertTrue(array_equal(around(
markov_model.p_emission, decimals=3),
around(output_p_emission, decimals=3)))
def test_forward(self):
states = ["CP", "IP"]
outputs = [2, 1, 0]
lp_initial = log([1.0, 0.0000001])
lp_transition = log([[0.7, 0.3], [0.5, 0.5]])
lp_emission = log([[0.6, 0.1, 0.3], [0.1, 0.7, 0.2]])
matrix = array([[0., -1.5606477, -3.07477539, -3.84932984],
[-16.11809565, -2.4079455, -3.27544608, -4.5847794]])
self.assertTrue(
array_equal(around(MarkovModel._forward(len(states), len(outputs),
lp_initial,
lp_transition,
lp_emission,
outputs), decimals=3),
around(matrix, decimals=3)))
def test_backward(self):
states = ["CP", "IP"]
outputs = [2, 1, 0]
lp_transition = log([[0.7, 0.3], [0.5, 0.5]])
lp_emission = log([[0.6, 0.1, 0.3], [0.1, 0.7, 0.2]])
matrix = array([[-3.45776773, -3.10109279, -0.51082562, 0.],
[-3.54045945, -1.40649707, -2.30258509, 0.]])
self.assertTrue(
array_equal(around(MarkovModel._backward(
len(states), len(outputs), lp_transition, lp_emission, outputs), decimals=3),
around(matrix, decimals=3)))
def test_mle(self):
states = ["0", "1", "2", "3"]
alphabet = ["A", "C", "G", "T"]
training_data = [("AACCCGGGTTTTTTT", "001112223333333"),
("ACCGTTTTTTT", "01123333333"),
("ACGGGTTTTTT", "01222333333"),
("ACCGTTTTTTTT", "011233333333"), ]
training_outputs = array([[0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3], [
0, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3], [0, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3], [0, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3]])
training_states = array([[0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3], [
0, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3], [0, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3], [0, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3]])
p_initial = array([1., 0., 0., 0.])
p_transition = array([[0.2, 0.8, 0., 0.],
[0., 0.5, 0.5, 0.],
[0., 0., 0.5, 0.5],
[0., 0., 0., 1.]])
p_emission = array(
[[0.66666667, 0.11111111, 0.11111111, 0.11111111],
[0.08333333, 0.75, 0.08333333, 0.08333333],
[0.08333333, 0.08333333, 0.75, 0.08333333],
[0.03125, 0.03125, 0.03125, 0.90625]])
p_initial_out, p_transition_out, p_emission_out = MarkovModel._mle(
len(states), len(alphabet), training_outputs, training_states, None, None, None)
self.assertTrue(
array_equal(around(p_initial_out, decimals=3), around(p_initial, decimals=3)))
self.assertTrue(
array_equal(around(p_transition_out, decimals=3), around(p_transition, decimals=3)))
self.assertTrue(
array_equal(around(p_emission_out, decimals=3), around(p_emission, decimals=3)))
def test_argmaxes(self):
matrix = array([[4, 5, 6], [9, 7, 8], [1, 2, 3]])
output = [3]
self.assertEqual(len(MarkovModel._argmaxes(matrix)), len(output))
self.assertEqual(MarkovModel._argmaxes(matrix)[0], output[0])
def test_viterbi(self):
states = ["CP", "IP"]
outputs = [2, 1, 0]
lp_initial = log([1.0, 0.0000001])
lp_transition = log([[0.7, 0.3], [0.5, 0.5]])
lp_emission = log([[0.6, 0.1, 0.3], [0.1, 0.7, 0.2]])
output1 = [0, 1, 0]
output2 = -3.968593356916541
viterbi_output = MarkovModel._viterbi(
len(states), lp_initial, lp_transition,
lp_emission, outputs)
self.assertEqual(len(viterbi_output[0][0]), 3)
self.assertEqual(viterbi_output[0][0][0], output1[0])
self.assertEqual(viterbi_output[0][0][1], output1[1])
self.assertEqual(viterbi_output[0][0][2], output1[2])
self.assertEqual(
float("%.3f" % viterbi_output[0][1]),
float("%.3f" % output2))
def test_normalize_and_copy_and_check(self):
matrix_in1 = array(
[[1.1, 2.2, 3.3], [4.4, 5.5, 6.6], [7.7, 8.8, 9.9]])
matrix_in2 = array([1, 2, 3])
matrix_out1 = array(
[[0.16666667, 0.33333333, 0.5], [0.26666667, 0.33333333, 0.4], [0.29166667, 0.33333333, 0.375]])
matrix_out2 = array([0.16666667, 0.33333333, 0.5])
self.assertTrue(
array_equal(around(MarkovModel._normalize(matrix_in1), decimals=3), around(matrix_out1, decimals=3)))
self.assertTrue(
array_equal(around(MarkovModel._normalize(matrix_in2), decimals=3), around(matrix_out2, decimals=3)))
shape1 = (3, 3)
shape2 = (3,)
self.assertTrue(
array_equal(around(MarkovModel._copy_and_check(matrix_out1, shape1), decimals=3), around(matrix_out1, decimals=3)))
self.assertTrue(
array_equal(around(MarkovModel._copy_and_check(matrix_out2, shape2), decimals=3), around(matrix_out2, decimals=3)))
def test_uniform_norm(self):
shape = (4, 3)
matrix = array([[0.33333333, 0.33333333, 0.33333333],
[0.33333333, 0.33333333, 0.33333333],
[0.33333333, 0.33333333, 0.33333333],
[0.33333333, 0.33333333, 0.33333333]])
self.assertTrue(
array_equal(around(MarkovModel._uniform_norm(shape), decimals=3), around(matrix, decimals=3)))
def test_random_norm(self):
random.seed(0)
shape = (4, 3)
matrix = array([[0.29399155, 0.38311672, 0.32289173],
[0.33750765, 0.26241723, 0.40007512],
[0.1908342, 0.38890714, 0.42025866],
[0.22501625, 0.46461061, 0.31037314]])
self.assertTrue(
array_equal(around(MarkovModel._random_norm(shape), decimals=3), around(matrix, decimals=3)))
def test_logsum_and_exp_logsum(self):
matrix = array(
[[1.1, 2.2, 3.3], [4.4, 5.5, 6.6], [7.7, 8.8, 9.9]])
matrix1 = array([1, 2, 3])
output = 10.304721798
output1 = 3.40760596444
self.assertEqual(
float("%.3f" % MarkovModel._logsum(matrix)),
float("%.3f" % output))
self.assertEqual(
float("%.3f" % MarkovModel._logsum(matrix1)),
float("%.3f" % output1))
output2 = 29873.342245
output3 = 30.1928748506
self.assertEqual(
float("%.3f" % MarkovModel._exp_logsum(matrix)),
float("%.3f" % output2))
self.assertEqual(
float("%.3f" % MarkovModel._exp_logsum(matrix1)),
float("%.3f" % output3))
def test_logvecadd(self):
vec1 = log(array([1, 2, 3, 4]))
vec2 = log(array([5, 6, 7, 8]))
sumvec = array([1.79175947, 2.07944154, 2.30258509, 2.48490665])
self.assertTrue(
array_equal(around(MarkovModel._logvecadd(vec1, vec2), decimals=3), around(sumvec, decimals=3)))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)