def test_pathoscope_em_4(self):
U = {2: 1}
NU = {0: [[0, 1], [50, 50], [0.5, 0.5]], 1: [[0, 1], [50, 50], [0.5, 0.5]],
3: [[2, 3], [50, 50], [0.5, 0.5]], 4: [[2, 0], [50, 50], [0.5, 0.5]]}
### Genome hash
genomes = {0:"genome3", 1:"genome4", 2:"genome1", 3:"genome2"}
(initPi, pi, theta, NU) = PathoID.pathoscope_em(U, NU, genomes, self.maxIter, self.emEpsilon, self.verbose)
print initPi, pi, theta, NU
expectedInitPi = [0.3, 0.4, 0.2, 0.1]
for j in range(len(expectedInitPi)):
self.assertAlmostEquals(initPi[j], expectedInitPi[j], 4, "Failed EM Example 4 Initial PI Assertion j=%d" %j)
expectedPi = [0.57, 0.20, 0.23, 0.0]
for j in range(len(expectedPi)):
self.assertAlmostEquals(pi[j], expectedPi[j], 2, "Failed EM Example 4 PI Assertion")
expectedTheta = [0.72, 0.0, 0.28, 0.0]
for j in range(len(expectedTheta)):
self.assertAlmostEquals(theta[j], expectedTheta[j], 2, "Failed EM Example 4 Theta Assertion")
expectedNU = {0: [[0, 1], [50, 50], [1.0, 0.0]], 1: [[0, 1], [50, 50], [1.0, 0.0]],
3: [[2, 3], [50, 50], [1.0, 0.0]], 4: [[2, 0], [50, 50], [0.14, 0.86]]}
for read in expectedNU:
self.assertEquals(NU[read][0], expectedNU[read][0],
"Failed EM Example 4 Non-Unique Read %d genome mapping Assertion" %read)
self.assertEquals(NU[read][1], expectedNU[read][1],
"Failed EM Example 4 Non-Unique Read %d score Assertion" %read)
for j in range(len(expectedNU[read][2])):
self.assertAlmostEquals(NU[read][2][j], expectedNU[read][2][j], 2,
"Failed EM Example 4 Non-Unique Read %d proportion Assertion" %read)
def test_pathoscope_em_3(self):
U = {0: 0, 1: 0, 2: 0, 3: 1, 4: 1}
NU = {5: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
6: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
7: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]]}
### Genome hash
genomes = {0:"genome1", 1:"genome2", 2:"genome3"}
(initPi, pi, theta, NU) = PathoID.pathoscope_em(U, NU, genomes, self.maxIter, self.emEpsilon, self.verbose)
print initPi, pi, theta, NU
expectedInitPi = [0.5, 0.375, 0.125]
for j in range(len(expectedInitPi)):
self.assertAlmostEquals(initPi[j], expectedInitPi[j], 4, "Failed EM Example 3 Initial PI Assertion j=%d" %j)
expectedPi = [0.75, 0.25, 0.0]
for j in range(len(expectedPi)):
self.assertAlmostEquals(pi[j], expectedPi[j], 2, "Failed EM Example 3 PI Assertion")
expectedTheta = [1.0, 0.0, 0.0]
for j in range(len(expectedTheta)):
self.assertAlmostEquals(theta[j], expectedTheta[j], 2, "Failed EM Example 3 Theta Assertion")
expectedNU = {5: [[0, 1, 2], [33, 33, 33], [1.0, 0.0, 0.0]],
6: [[0, 1, 2], [33, 33, 33], [1.0, 0.0, 0.0]],
7: [[0, 1, 2], [33, 33, 33], [1.0, 0.0, 0.0]]}
for read in expectedNU:
self.assertEquals(NU[read][0], expectedNU[read][0],
"Failed EM Example 3 Non-Unique Read %d genome mapping Assertion" %read)
self.assertEquals(NU[read][1], expectedNU[read][1],
"Failed EM Example 3 Non-Unique Read %d score Assertion" %read)
for j in range(len(expectedNU[read][2])):
self.assertAlmostEquals(NU[read][2][j], expectedNU[read][2][j], 2,
"Failed EM Example 3 Non-Unique Read %d proportion Assertion" %read)
def test_pathoscope_em_2(self):
U = {}
NU = {
0: [[0, 1], [50, 50], [0.5, 0.5]],
1: [[0, 1], [50, 50], [0.5, 0.5]],
2: [[0, 2], [50, 50], [0.5, 0.5]],
3: [[0, 2], [50, 50], [0.5, 0.5]],
4: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
5: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
6: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]]
}
### Genome hash
genomes = {0: "genome1", 1: "genome2", 2: "genome3"}
(initPi, pi, theta,
NU) = PathoID.pathoscope_em(U, NU, genomes, self.maxIter,
self.emEpsilon, self.verbose)
print initPi, pi, theta, NU
expectedInitPi = [0.4286, 0.2857, 0.2857]
for j in range(len(expectedInitPi)):
self.assertAlmostEquals(
initPi[j], expectedInitPi[j], 4,
"Failed EM Example 2 Initial PI Assertion j=%d" % j)
expectedPi = [1.0, 0.0, 0.0]
for j in range(len(expectedPi)):
self.assertAlmostEquals(pi[j], expectedPi[j], 4,
"Failed EM Example 2 PI Assertion")
expectedTheta = [1.0, 0.0, 0.0]
for j in range(len(expectedTheta)):
self.assertAlmostEquals(theta[j], expectedTheta[j], 4,
"Failed EM Example 2 Theta Assertion")
expectedNU = {
0: [[0, 1], [50, 50], [1.0, 0.0]],
1: [[0, 1], [50, 50], [1.0, 0.0]],
2: [[0, 2], [50, 50], [1.0, 0.0]],
3: [[0, 2], [50, 50], [1.0, 0.0]],
4: [[0, 1, 2], [33, 33, 33], [1.0, 0.0, 0.0]],
5: [[0, 1, 2], [33, 33, 33], [1.0, 0.0, 0.0]],
6: [[0, 1, 2], [33, 33, 33], [1.0, 0.0, 0.0]]
}
for read in expectedNU:
self.assertEquals(
NU[read][0], expectedNU[read][0],
"Failed EM Example 2 Non-Unique Read %d genome mapping Assertion"
% read)
self.assertEquals(
NU[read][1], expectedNU[read][1],
"Failed EM Example 2 Non-Unique Read %d score Assertion" %
read)
for j in range(len(expectedNU[read][2])):
self.assertAlmostEquals(
NU[read][2][j], expectedNU[read][2][j], 4,
"Failed EM Example 2 Non-Unique Read %d proportion Assertion"
% read)
def test_pathoscope_em_4(self):
U = {2: 1}
NU = {
0: [[0, 1], [50, 50], [0.5, 0.5]],
1: [[0, 1], [50, 50], [0.5, 0.5]],
3: [[2, 3], [50, 50], [0.5, 0.5]],
4: [[2, 0], [50, 50], [0.5, 0.5]]
}
### Genome hash
genomes = {0: "genome3", 1: "genome4", 2: "genome1", 3: "genome2"}
(initPi, pi, theta,
NU) = PathoID.pathoscope_em(U, NU, genomes, self.maxIter,
self.emEpsilon, self.verbose)
print initPi, pi, theta, NU
expectedInitPi = [0.3, 0.4, 0.2, 0.1]
for j in range(len(expectedInitPi)):
self.assertAlmostEquals(
initPi[j], expectedInitPi[j], 4,
"Failed EM Example 4 Initial PI Assertion j=%d" % j)
expectedPi = [0.57, 0.20, 0.23, 0.0]
for j in range(len(expectedPi)):
self.assertAlmostEquals(pi[j], expectedPi[j], 2,
"Failed EM Example 4 PI Assertion")
expectedTheta = [0.72, 0.0, 0.28, 0.0]
for j in range(len(expectedTheta)):
self.assertAlmostEquals(theta[j], expectedTheta[j], 2,
"Failed EM Example 4 Theta Assertion")
expectedNU = {
0: [[0, 1], [50, 50], [1.0, 0.0]],
1: [[0, 1], [50, 50], [1.0, 0.0]],
3: [[2, 3], [50, 50], [1.0, 0.0]],
4: [[2, 0], [50, 50], [0.14, 0.86]]
}
for read in expectedNU:
self.assertEquals(
NU[read][0], expectedNU[read][0],
"Failed EM Example 4 Non-Unique Read %d genome mapping Assertion"
% read)
self.assertEquals(
NU[read][1], expectedNU[read][1],
"Failed EM Example 4 Non-Unique Read %d score Assertion" %
read)
for j in range(len(expectedNU[read][2])):
self.assertAlmostEquals(
NU[read][2][j], expectedNU[read][2][j], 2,
"Failed EM Example 4 Non-Unique Read %d proportion Assertion"
% read)
