class Test_BiasMat(TestCase):
"""test construction of BiasMat"""
def setUp(self):
"""setup Test_BiasMat class with construction of a biasmat"""
bed_list = ChunkList.read('example/example.bed')
self.chunk = bed_list[0]
self.biastrack = InsertionBiasTrack(self.chunk.chrom, self.chunk.start, self.chunk.end)
self.biastrack.read_track('example/example.Scores.bedgraph.gz')
self.biasmat = BiasMat2D(self.chunk.chrom,self.chunk.start+100,self.chunk.end-100,100,200)
self.biasmat.makeBiasMat(self.biastrack)
def test_biasmat1(self):
"""test case1 for biasmat"""
a1 = self.biastrack.get(pos = self.biasmat.start - 49)
a2 = self.biastrack.get(pos = self.biasmat.start + 50)
correct = np.exp(a1+a2)
self.assertTrue(abs(correct - self.biasmat.mat[0,0])<0.01*correct)
def test_biasmat2(self):
"""test case2 for biasmat"""
a1 = self.biastrack.get(pos = self.biasmat.start + 145)
a2 = self.biastrack.get(pos = self.biasmat.start + 295)
correct = np.exp(a1+a2)
self.assertTrue(abs(correct - self.biasmat.mat[51,220]) < 0.01*correct)
def test_normByInsertDist(self):
"""test that normalization by insert distribution works as expected"""
isizes = FragmentSizes(lower=100,upper=200, vals = np.array(range(100,200)))
self.biasmat.normByInsertDist(isizes)
a1 = self.biastrack.get(pos = self.biasmat.start -50)
a2 = self.biastrack.get(pos = self.biasmat.start + 50)
correct = np.exp(a1+a2)*isizes.get(size = 101)
self.assertTrue(abs(correct - self.biasmat.mat[1,0])<0.01*correct)
class Test_BiasMat(TestCase):
"""test construction of BiasMat"""
def setUp(self):
"""setup Test_BiasMat class with construction of a biasmat"""
bed_list = ChunkList.read('example/example.bed')
self.chunk = bed_list[0]
self.biastrack = InsertionBiasTrack(self.chunk.chrom, self.chunk.start,
self.chunk.end)
self.biastrack.read_track('example/example.Scores.bedgraph.gz')
self.biasmat = BiasMat2D(self.chunk.chrom, self.chunk.start + 100,
self.chunk.end - 100, 100, 200)
self.biasmat.makeBiasMat(self.biastrack)
def test_biasmat1(self):
"""test case1 for biasmat"""
a1 = self.biastrack.get(pos=self.biasmat.start - 49)
a2 = self.biastrack.get(pos=self.biasmat.start + 50)
correct = np.exp(a1 + a2)
self.assertTrue(abs(correct - self.biasmat.mat[0, 0]) < 0.01 * correct)
def test_biasmat2(self):
"""test case2 for biasmat"""
a1 = self.biastrack.get(pos=self.biasmat.start + 145)
a2 = self.biastrack.get(pos=self.biasmat.start + 295)
correct = np.exp(a1 + a2)
self.assertTrue(
abs(correct - self.biasmat.mat[51, 220]) < 0.01 * correct)
def test_normByInsertDist(self):
"""test that normalization by insert distribution works as expected"""
isizes = FragmentSizes(lower=100,
upper=200,
vals=np.array(range(100, 200)))
self.biasmat.normByInsertDist(isizes)
a1 = self.biastrack.get(pos=self.biasmat.start - 50)
a2 = self.biastrack.get(pos=self.biasmat.start + 50)
correct = np.exp(a1 + a2) * isizes.get(size=101)
self.assertTrue(abs(correct - self.biasmat.mat[1, 0]) < 0.01 * correct)
