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_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")
