def run_pathoscope(log, sam, sample, outdir):
log.info("Running pathoscope")
out_matrix = False
verbose = False
score_cutoff = 0.01
exp_tag = sample
ali_format = "sam"
emEpsilon = 1e-7
maxIter = 50
PathoID.pathoscope_reassign(
out_matrix, verbose, score_cutoff, exp_tag, ali_format, sam, outdir, emEpsilon, maxIter, True
)
def test_conv_align2GRmat_bl8_2(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex2.bl8'
aliFormat = 2
(U, NU, genomes, reads) = PathoID.conv_align2GRmat(ali_file,self.scoreCutoff,aliFormat)
print U, NU, genomes, reads
expectedU = {}
self.assertEquals(expectedU, U, "Failed bl8 Example 2 Unique Reads Assertion")
expectedNU = {0: [[0, 1], [703681821, 703681821], [0.5, 0.5]],
1: [[0, 1], [703681821, 703681821], [0.5, 0.5]],
2: [[2, 1], [703681821, 703681821], [0.5, 0.5]],
3: [[2, 1], [703681821, 703681821], [0.5, 0.5]],
4: [[2, 0, 1], [703681821, 703681821, 703681821], [0.3333, 0.3333, 0.3333]],
5: [[2, 0, 1], [703681821, 703681821, 703681821], [0.3333, 0.3333, 0.3333]],
6: [[2, 0, 1], [703681821, 703681821, 703681821], [0.3333, 0.3333, 0.3333]]}
for read in expectedNU:
self.assertEquals(expectedNU[read][0], NU[read][0],
"Failed bl8 Example 2 Non-Unique Read %d genome mapping Assertion" %read)
self.assertEquals(expectedNU[read][1], NU[read][1],
"Failed bl8 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 bl8 Example 2 Non-Unique Read %d proportion Assertion" %read)
expectedGenomes = ['genome2', 'genome1', 'genome3']
self.assertEquals(expectedGenomes, genomes, "Failed bl8 Example 2 Genomes Assertion")
expectedReads = ['read1_12', 'read2_12', 'read3_13', 'read4_13', 'read5_123', 'read6_123', 'read7_123']
self.assertEquals(expectedReads, reads, "Failed bl8 Example 2 Reads Assertion")
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)
def test_conv_align2GRmat_bl8_2(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex2.bl8'
aliFormat = 2
(U, NU, genomes,
reads) = PathoID.conv_align2GRmat(ali_file, self.scoreCutoff,
aliFormat)
print U, NU, genomes, reads
expectedU = {}
self.assertEquals(expectedU, U,
"Failed bl8 Example 2 Unique Reads Assertion")
expectedNU = {
0: [[0, 1], [703681821, 703681821], [0.5, 0.5]],
1: [[0, 1], [703681821, 703681821], [0.5, 0.5]],
2: [[2, 1], [703681821, 703681821], [0.5, 0.5]],
3: [[2, 1], [703681821, 703681821], [0.5, 0.5]],
4: [[2, 0, 1], [703681821, 703681821, 703681821],
[0.3333, 0.3333, 0.3333]],
5: [[2, 0, 1], [703681821, 703681821, 703681821],
[0.3333, 0.3333, 0.3333]],
6: [[2, 0, 1], [703681821, 703681821, 703681821],
[0.3333, 0.3333, 0.3333]]
}
for read in expectedNU:
self.assertEquals(
expectedNU[read][0], NU[read][0],
"Failed bl8 Example 2 Non-Unique Read %d genome mapping Assertion"
% read)
self.assertEquals(
expectedNU[read][1], NU[read][1],
"Failed bl8 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 bl8 Example 2 Non-Unique Read %d proportion Assertion"
% read)
expectedGenomes = ['genome2', 'genome1', 'genome3']
self.assertEquals(expectedGenomes, genomes,
"Failed bl8 Example 2 Genomes Assertion")
expectedReads = [
'read1_12', 'read2_12', 'read3_13', 'read4_13', 'read5_123',
'read6_123', 'read7_123'
]
self.assertEquals(expectedReads, reads,
"Failed bl8 Example 2 Reads Assertion")
def test_conv_align2GRmat_sam_4(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex4.sam'
aliFormat = 1
(U, NU, genomes,
reads) = PathoID.conv_align2GRmat(ali_file, self.scoreCutoff,
aliFormat)
print U, NU, genomes, reads
expectedU = {2: 0}
self.assertEquals(expectedU, U,
"Failed sam Example 4 Unique Reads Assertion")
expectedNU = {
0: [[0, 1], [21, 21], [0.5, 0.5]],
1: [[1, 0], [21, 21], [0.5, 0.5]],
3: [[2, 3], [21, 21], [0.5, 0.5]],
4: [[2, 1], [21, 21], [0.5, 0.5]]
}
for read in expectedNU:
self.assertEquals(
expectedNU[read][0], NU[read][0],
"Failed sam Example 4 Non-Unique Read %d genome mapping Assertion"
% read)
self.assertEquals(
expectedNU[read][1], NU[read][1],
"Failed sam 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], 4,
"Failed sam Example 4 Non-Unique Read %d proportion Assertion"
% read)
expectedGenomes = ['genome4', 'genome3', 'genome1', 'genome2']
self.assertEquals(expectedGenomes, genomes,
"Failed sam Example 4 Genomes Assertion")
expectedReads = [
'read1_34', 'read2_34', 'read3_4', 'read4_12', 'read5_13'
]
self.assertEquals(expectedReads, reads,
"Failed sam Example 4 Reads Assertion")
def test_conv_align2GRmat_sam_3(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex3.sam'
aliFormat = 1
(U, NU, genomes,
reads) = PathoID.conv_align2GRmat(ali_file, self.scoreCutoff,
aliFormat)
print U, NU, genomes, reads
expectedU = {0: 0, 1: 0, 2: 0, 3: 1, 4: 1}
self.assertEquals(expectedU, U,
"Failed sam Example 3 Unique Reads Assertion")
expectedNU = {
5: [[2, 0, 1], [21, 21, 21], [0.3333, 0.3333, 0.3333]],
6: [[1, 0, 2], [21, 21, 21], [0.3333, 0.3333, 0.3333]],
7: [[2, 1, 0], [21, 21, 21], [0.3333, 0.3333, 0.3333]]
}
for read in expectedNU:
self.assertEquals(
expectedNU[read][0], NU[read][0],
"Failed sam Example 3 Non-Unique Read %d genome mapping Assertion"
% read)
self.assertEquals(
expectedNU[read][1], NU[read][1],
"Failed sam 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], 4,
"Failed sam Example 3 Non-Unique Read %d proportion Assertion"
% read)
expectedGenomes = ['genome1', 'genome2', 'genome3']
self.assertEquals(expectedGenomes, genomes,
"Failed sam Example 3 Genomes Assertion")
expectedReads = [
'read1_1', 'read2_1', 'read3_1', 'read4_3', 'read5_2', 'read6_123',
'read7_123', 'read8_123'
]
self.assertEquals(expectedReads, reads,
"Failed sam Example 3 Reads Assertion")
def test_conv_align2GRmat_sam_4(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex4.sam'
aliFormat = 1
(U, NU, genomes, reads) = PathoID.conv_align2GRmat(ali_file,self.scoreCutoff,aliFormat)
print U, NU, genomes, reads
expectedU = {2: 0}
self.assertEquals(expectedU, U, "Failed sam Example 4 Unique Reads Assertion")
expectedNU = {0: [[0, 1], [21, 21], [0.5, 0.5]], 1: [[1, 0], [21, 21], [0.5, 0.5]],
3: [[2, 3], [21, 21], [0.5, 0.5]], 4: [[2, 1], [21, 21], [0.5, 0.5]]}
for read in expectedNU:
self.assertEquals(expectedNU[read][0], NU[read][0],
"Failed sam Example 4 Non-Unique Read %d genome mapping Assertion" %read)
self.assertEquals(expectedNU[read][1], NU[read][1],
"Failed sam 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], 4,
"Failed sam Example 4 Non-Unique Read %d proportion Assertion" %read)
expectedGenomes = ['genome4', 'genome3', 'genome1', 'genome2']
self.assertEquals(expectedGenomes, genomes, "Failed sam Example 4 Genomes Assertion")
expectedReads = ['read1_34', 'read2_34', 'read3_4', 'read4_12', 'read5_13']
self.assertEquals(expectedReads, reads, "Failed sam Example 4 Reads Assertion")
def test_conv_align2GRmat_gsam_1(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex1.g.sam'
aliFormat = 0
(U, NU, genomes,
reads) = PathoID.conv_align2GRmat(ali_file, self.scoreCutoff,
aliFormat)
print U, NU, genomes, reads
expectedU = {0: 0, 1: 0}
self.assertEquals(expectedU, U,
"Failed gnusam Example 1 Unique Reads Assertion")
expectedNU = {
2: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
3: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
4: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]]
}
for read in expectedNU:
self.assertEquals(
expectedNU[read][0], NU[read][0],
"Failed gnusam Example 1 Non-Unique Read %d genome mapping Assertion"
% read)
self.assertEquals(
expectedNU[read][1], NU[read][1],
"Failed gnusam Example 1 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 gnusam Example 1 Non-Unique Read %d proportion Assertion"
% read)
expectedGenomes = ['genome1', 'genome2', 'genome3']
self.assertEquals(expectedGenomes, genomes,
"Failed gnusam Example 1 Genomes Assertion")
expectedReads = [
'read1_1', 'read2_1', 'read3_123', 'read4_123', 'read5_123'
]
self.assertEquals(expectedReads, reads,
"Failed gnusam Example 1 Reads Assertion")
def test_conv_align2GRmat_sam_3(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex3.sam'
aliFormat = 1
(U, NU, genomes, reads) = PathoID.conv_align2GRmat(ali_file,self.scoreCutoff,aliFormat)
print U, NU, genomes, reads
expectedU = {0: 0, 1: 0, 2: 0, 3: 1, 4: 1}
self.assertEquals(expectedU, U, "Failed sam Example 3 Unique Reads Assertion")
expectedNU = {5: [[2, 0, 1], [21, 21, 21], [0.3333, 0.3333, 0.3333]],
6: [[1, 0, 2], [21, 21, 21], [0.3333, 0.3333, 0.3333]],
7: [[2, 1, 0], [21, 21, 21], [0.3333, 0.3333, 0.3333]]}
for read in expectedNU:
self.assertEquals(expectedNU[read][0], NU[read][0],
"Failed sam Example 3 Non-Unique Read %d genome mapping Assertion" %read)
self.assertEquals(expectedNU[read][1], NU[read][1],
"Failed sam 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], 4,
"Failed sam Example 3 Non-Unique Read %d proportion Assertion" %read)
expectedGenomes = ['genome1', 'genome2', 'genome3']
self.assertEquals(expectedGenomes, genomes, "Failed sam Example 3 Genomes Assertion")
expectedReads = ['read1_1', 'read2_1', 'read3_1', 'read4_3', 'read5_2', 'read6_123', 'read7_123', 'read8_123']
self.assertEquals(expectedReads, reads, "Failed sam Example 3 Reads Assertion")
def test_conv_align2GRmat_gsam_1(self):
currentdir = os.path.dirname(os.path.abspath(__file__))
ali_file = currentdir + os.sep + 'data' + os.sep + 'ex1.g.sam'
aliFormat = 0
(U, NU, genomes, reads) = PathoID.conv_align2GRmat(ali_file,self.scoreCutoff,aliFormat)
print U, NU, genomes, reads
expectedU = {0: 0, 1: 0}
self.assertEquals(expectedU, U, "Failed gnusam Example 1 Unique Reads Assertion")
expectedNU = {2: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
3: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]],
4: [[0, 1, 2], [33, 33, 33], [0.3333, 0.3333, 0.3333]]}
for read in expectedNU:
self.assertEquals(expectedNU[read][0], NU[read][0],
"Failed gnusam Example 1 Non-Unique Read %d genome mapping Assertion" %read)
self.assertEquals(expectedNU[read][1], NU[read][1],
"Failed gnusam Example 1 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 gnusam Example 1 Non-Unique Read %d proportion Assertion" %read)
expectedGenomes = ['genome1', 'genome2', 'genome3']
self.assertEquals(expectedGenomes, genomes, "Failed gnusam Example 1 Genomes Assertion")
expectedReads = ['read1_1', 'read2_1', 'read3_123', 'read4_123', 'read5_123']
self.assertEquals(expectedReads, reads, "Failed gnusam Example 1 Reads Assertion")
default='testset',
dest='exp_tag',
help='Experiment tag')
parser.add_argument('-outdir',
action='store',
default='.',
dest='outdir',
help='Output Directory')
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
parser.add_argument('-t',
action='store',
default='sam',
dest='ali_format',
help='Alignment Format: sam/bl8/gnu-sam')
parser.add_argument('-f',
action='store',
dest='ali_file',
required=True,
help='Alignment file path')
inputArgs = parser.parse_args()
start = time()
PathoID.pathoscope_reassign(inputArgs.out_matrix, inputArgs.verbose,
inputArgs.score_cutoff, inputArgs.exp_tag,
inputArgs.ali_format, inputArgs.ali_file,
inputArgs.outdir, inputArgs.emEpsilon,
inputArgs.maxIter, not (inputArgs.noalign))
elapsed = time() - start
if inputArgs.verbose:
print "EM Elapsed Time: %d" % (elapsed)
parser.add_argument('-o', action='store_true', default=False, dest='out_matrix',
help='Output alignment matrix')
parser.add_argument('-noUpdatedAlignFile', action='store_true', default=False, dest='noalign',
help='Do not generate an updated alignment file')
parser.add_argument('-verbose', action='store_true', default=False, dest='verbose',
help='Prints verbose text while running')
parser.add_argument('-s', action='store', default=0.01, type=float,
dest='score_cutoff', help='Score Cutoff')
parser.add_argument('-emEpsilon', action='store', default=1e-7, type=float,
dest='emEpsilon', help='EM Algorithm Epsilon cutoff')
parser.add_argument('-maxIter', action='store', default=50, type=int,
dest='maxIter', help='EM Algorithm maximum iterations')
parser.add_argument('-e', action='store', default='testset', dest='exp_tag',
help='Experiment tag')
parser.add_argument('-outdir', action='store', default='.', dest='outdir',
help='Output Directory')
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
parser.add_argument('-t', action='store', default='sam', dest='ali_format',
help='Alignment Format: sam/bl8/gnu-sam')
parser.add_argument('-f', action='store', dest='ali_file', required=True,
help='Alignment file path')
inputArgs = parser.parse_args()
start = time();
PathoID.pathoscope_reassign(inputArgs.out_matrix, inputArgs.verbose,
inputArgs.score_cutoff, inputArgs.exp_tag, inputArgs.ali_format, inputArgs.ali_file,
inputArgs.outdir, inputArgs.emEpsilon, inputArgs.maxIter, not(inputArgs.noalign))
elapsed = time() - start;
if inputArgs.verbose:
print "EM Elapsed Time: %d" % (elapsed)
