def test_occupancy_calc3(self):
"""test average occupancy for when you have 40 random reads,
which should be 75% from nuc dist
"""
results = np.zeros(100)
upper = np.zeros(100)
lower = np.zeros(100)
for i in range(100):
a = np.random.multinomial(10,self.fragment_dist.nfr_fit.get())
b = np.random.multinomial(30,self.fragment_dist.nuc_fit.get())
results[i],lower[i],upper[i] = calculateOccupancy(a+b,np.array([1,1,1]),self.params)
print np.mean(results)
self.assertTrue(abs(np.mean(results)-0.75)<0.1)
self.assertTrue(sum(upper < 0.75) < 85)
self.assertTrue(sum(lower > 0.75) < 85)
def test_occupancy_calc3(self):
"""test average occupancy for when you have 40 random reads,
which should be 75% from nuc dist
"""
results = np.zeros(100)
upper = np.zeros(100)
lower = np.zeros(100)
for i in range(100):
a = np.random.multinomial(10, self.fragment_dist.nfr_fit.get())
b = np.random.multinomial(30, self.fragment_dist.nuc_fit.get())
results[i], lower[i], upper[i] = calculateOccupancy(
a + b, np.array([1, 1, 1]), self.params)
print np.mean(results)
self.assertTrue(abs(np.mean(results) - 0.75) < 0.1)
self.assertTrue(sum(upper < 0.75) < 85)
self.assertTrue(sum(lower > 0.75) < 85)
def test_occupancy_calc4(self):
"""test average occupancy for when you have 40 random reads,
which should be 75% from nuc dist. include some bias
"""
results = np.zeros(100)
upper = np.zeros(100)
lower = np.zeros(100)
bias = np.array([3,2,1])
nfrprob = self.fragment_dist.nfr_fit.get() * bias
nucprob = self.fragment_dist.nuc_fit.get() * bias
nucprob = nucprob / np.sum(nucprob)
nfrprob = nfrprob / np.sum(nfrprob)
for i in range(100):
a = np.random.multinomial(10,nfrprob)
b = np.random.multinomial(30,nucprob)
results[i],lower[i],upper[i] = calculateOccupancy(a+b,bias,self.params)
print np.mean(results)
self.assertTrue(abs(np.mean(results)-0.75)<0.1)
self.assertTrue(sum(upper < 0.75) < 85)
self.assertTrue(sum(lower > 0.75) < 85)
def test_occupancy_calc4(self):
"""test average occupancy for when you have 40 random reads,
which should be 75% from nuc dist. include some bias
"""
results = np.zeros(100)
upper = np.zeros(100)
lower = np.zeros(100)
bias = np.array([3, 2, 1])
nfrprob = self.fragment_dist.nfr_fit.get() * bias
nucprob = self.fragment_dist.nuc_fit.get() * bias
nucprob = nucprob / np.sum(nucprob)
nfrprob = nfrprob / np.sum(nfrprob)
for i in range(100):
a = np.random.multinomial(10, nfrprob)
b = np.random.multinomial(30, nucprob)
results[i], lower[i], upper[i] = calculateOccupancy(
a + b, bias, self.params)
print np.mean(results)
self.assertTrue(abs(np.mean(results) - 0.75) < 0.1)
self.assertTrue(sum(upper < 0.75) < 85)
self.assertTrue(sum(lower > 0.75) < 85)
def test_occupancy_calc2(self):
"""test occupancy for a 50% occupancy situation"""
occ = calculateOccupancy(np.array([1, 1, 1]), np.array([1, 1, 1]),
self.params)
self.assertTrue(occ[0] == 0.5)
def test_occupancy_calc1(self):
"""test occupancy class for a zero occupancy situation"""
occ = calculateOccupancy(np.array([1, 0, 0]), np.array([1, 1, 1]),
self.params)
self.assertTrue(occ[0] == 0)
def test_occupancy_calc2(self):
"""test occupancy for a 50% occupancy situation"""
occ = calculateOccupancy(np.array([1,1,1]),np.array([1,1,1]),self.params)
self.assertTrue(occ[0] == 0.5)
def test_occupancy_calc1(self):
"""test occupancy class for a zero occupancy situation"""
occ = calculateOccupancy(np.array([1,0,0]),np.array([1,1,1]),self.params)
self.assertTrue(occ[0] == 0)