def test_cai_2(self):
"""cai_2 should produce expected results"""
ref_freqs = cu.copy()
ref_freqs.update({'AGA':4, 'AGG':2, 'CCC':5, 'CCA':1, 'UGG':1})
#tests with arithmetic mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean), 0.75)
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean), 0.6)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_2(ref_freqs_2, gene_freqs, average=arithmetic_mean)
vals = [1,1,1,.5,1,1,.2,1,.5,.5]
expect = sum(vals)/len(vals)
self.assertEqual(obs, expect)
#tests with geometric mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertFloatEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.5**5)**(0.1))
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertFloatEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.2**5)**0.1)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_2(ref_freqs_2, gene_freqs, average=geometric_mean)
vals = [1,1,1,.5,1,1,.2,1,.5,.5]
expect = (product(vals))**(1./len(vals))
self.assertEqual(obs, expect)
#test that results match example on Gang Wu's CAI calculator page
ref_freqs = cu.copy()
ref_freqs.update({'UUU':78743, 'UUC':56591, 'UUA':51320, 'UUG':45581, \
'CUU':42704, 'CUC':35873, 'CUA':15275, 'CUG':168885})
gene_freqs={'UUU':6, 'UUC':3, 'CUU':3, 'CUC':2, 'CUG':8}
self.assertFloatEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), \
exp((6*log(1) + 3*log(56591./78743) + 3*log(42704./168885) + \
2*log(35873./168885)+8*log(1))/22.))
def test_cai_1(self):
"""cai_1 should produce expected results"""
ref_freqs = cu.copy()
ref_freqs.update({'AGA':4, 'AGG':2, 'CCC':4, 'CCA':1, 'UGG':1})
#tests with arithmetic mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean), 0.75)
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean), 0.625)
ref_freqs_2 = cu.copy()
ref_freqs_2.update({'AGA':4, 'AGG':2, 'CCC':5, 'CCA':1, 'UGG':1})
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_1(ref_freqs_2, gene_freqs, average=arithmetic_mean)
vals = [.8,.8,.8,.4,1,1,.2,.4,.2,.2]
expect = sum(vals)/len(vals)
self.assertFloatEqual(obs, expect)
#tests with geometric mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertFloatEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.5**5)**(0.1))
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertFloatEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.25**5)**0.1)
ref_freqs_2 = cu.copy()
ref_freqs_2.update({'AGA':4, 'AGG':2, 'CCC':5, 'CCA':1, 'UGG':1})
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_1(ref_freqs_2, gene_freqs, average=geometric_mean)
vals = [.8,.8,.8,.4,1,1,.2,.4,.2,.2]
expect = (product(vals))**(1./len(vals))
self.assertFloatEqual(obs, expect)
def test_cai_3(self):
"""cai_3 should produce expected results"""
ref_freqs = cu.copy()
ref_freqs.update({'AGA':4, 'AGG':2, 'CCC':5, 'CCA':1, 'UGG':1})
#tests with arithmetic mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean), 0.75)
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean), 0.6)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_3(ref_freqs_2, gene_freqs, average=arithmetic_mean)
family_vals = [[1,1,1,.5],[1,1,.2],[1,.5,.5]]
family_averages = map(amean, family_vals)
expect = amean(family_averages)
self.assertEqual(obs, expect)
#tests with geometric mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.5**5)**(0.1))
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.2**5)**0.1)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_3(ref_freqs_2, gene_freqs, average=geometric_mean)
family_vals = [[1,1,1,.5],[1,1,.2],[1,.5,.5]]
family_averages = map(gmean, family_vals)
expect = gmean(family_averages)
self.assertEqual(obs, expect)
#tests with Eyre-Walker's variant -- should be same as geometric mean
gene_freqs = {'AGA':1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), 1)
gene_freqs = {'AGA':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), 1)
gene_freqs = {'AGG':5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), 0.5)
gene_freqs = {'AGG':5,'AGA':5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), \
(1**5 * 0.5**5)**(0.1))
gene_freqs={'AGA':5,'CCC':1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), 1)
gene_freqs={'AGA':5,'CCA':5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), \
(1**5 * 0.2**5)**0.1)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU':2,'UUC':1})
gene_freqs = {'AGA':3,'AGG':1,'CCC':2,'CCA':1,'UUU':1, 'UUC':2}
obs = cai_3(ref_freqs_2, gene_freqs, average='eyre_walker')
family_vals = [[1,1,1,.5],[1,1,.2],[1,.5,.5]]
family_averages = map(gmean, family_vals)
expect = gmean(family_averages)
self.assertEqual(obs, expect)
#test results for Gang Wu's example (unfortunately, no worked example for
#this model)
ref_freqs = cu.copy()
ref_freqs.update({'UUU':78743, 'UUC':56591, 'UUA':51320, 'UUG':45581, \
'CUU':42704, 'CUC':35873, 'CUA':15275, 'CUG':168885})
gene_freqs={'UUU':6, 'UUC':3, 'CUU':3, 'CUC':2, 'CUG':8}
obs = cai_3(ref_freqs, gene_freqs, average=geometric_mean)
family_vals = [6*[1]+3*[56591./78743],\
3*[42704./168885] + 2*[35873./168885]+8*[1]]
family_averages = map(gmean, family_vals)
expect = gmean(family_averages)
self.assertFloatEqual(obs, expect)
def test_cai_3(self):
"""cai_3 should produce expected results"""
ref_freqs = cu.copy()
ref_freqs.update({'AGA': 4, 'AGG': 2, 'CCC': 5, 'CCA': 1, 'UGG': 1})
#tests with arithmetic mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean),
0.75)
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=arithmetic_mean),
0.6)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_3(ref_freqs_2, gene_freqs, average=arithmetic_mean)
family_vals = [[1, 1, 1, .5], [1, 1, .2], [1, .5, .5]]
family_averages = map(amean, family_vals)
expect = amean(family_averages)
self.assertEqual(obs, expect)
#tests with geometric mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.5**5)**(0.1))
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.2**5)**0.1)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_3(ref_freqs_2, gene_freqs, average=geometric_mean)
family_vals = [[1, 1, 1, .5], [1, 1, .2], [1, .5, .5]]
family_averages = map(gmean, family_vals)
expect = gmean(family_averages)
self.assertEqual(obs, expect)
#tests with Eyre-Walker's variant -- should be same as geometric mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), \
(1**5 * 0.5**5)**(0.1))
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertFloatEqual(cai_3(ref_freqs, gene_freqs, average='eyre_walker'), \
(1**5 * 0.2**5)**0.1)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_3(ref_freqs_2, gene_freqs, average='eyre_walker')
family_vals = [[1, 1, 1, .5], [1, 1, .2], [1, .5, .5]]
family_averages = map(gmean, family_vals)
expect = gmean(family_averages)
self.assertEqual(obs, expect)
#test results for Gang Wu's example (unfortunately, no worked example for
#this model)
ref_freqs = cu.copy()
ref_freqs.update({'UUU':78743, 'UUC':56591, 'UUA':51320, 'UUG':45581, \
'CUU':42704, 'CUC':35873, 'CUA':15275, 'CUG':168885})
gene_freqs = {'UUU': 6, 'UUC': 3, 'CUU': 3, 'CUC': 2, 'CUG': 8}
obs = cai_3(ref_freqs, gene_freqs, average=geometric_mean)
family_vals = [6*[1]+3*[56591./78743],\
3*[42704./168885] + 2*[35873./168885]+8*[1]]
family_averages = map(gmean, family_vals)
expect = gmean(family_averages)
self.assertFloatEqual(obs, expect)
def test_cai_2(self):
"""cai_2 should produce expected results"""
ref_freqs = cu.copy()
ref_freqs.update({'AGA': 4, 'AGG': 2, 'CCC': 5, 'CCA': 1, 'UGG': 1})
#tests with arithmetic mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean),
0.75)
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=arithmetic_mean),
0.6)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_2(ref_freqs_2, gene_freqs, average=arithmetic_mean)
vals = [1, 1, 1, .5, 1, 1, .2, 1, .5, .5]
expect = sum(vals) / len(vals)
self.assertEqual(obs, expect)
#tests with geometric mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertFloatEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.5**5)**(0.1))
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertFloatEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.2**5)**0.1)
ref_freqs_2 = ref_freqs.copy()
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_2(ref_freqs_2, gene_freqs, average=geometric_mean)
vals = [1, 1, 1, .5, 1, 1, .2, 1, .5, .5]
expect = (product(vals))**(1. / len(vals))
self.assertEqual(obs, expect)
#test that results match example on Gang Wu's CAI calculator page
ref_freqs = cu.copy()
ref_freqs.update({'UUU':78743, 'UUC':56591, 'UUA':51320, 'UUG':45581, \
'CUU':42704, 'CUC':35873, 'CUA':15275, 'CUG':168885})
gene_freqs = {'UUU': 6, 'UUC': 3, 'CUU': 3, 'CUC': 2, 'CUG': 8}
self.assertFloatEqual(cai_2(ref_freqs, gene_freqs, average=geometric_mean), \
exp((6*log(1) + 3*log(56591./78743) + 3*log(42704./168885) + \
2*log(35873./168885)+8*log(1))/22.))
def test_cai_1(self):
"""cai_1 should produce expected results"""
ref_freqs = cu.copy()
ref_freqs.update({'AGA': 4, 'AGG': 2, 'CCC': 4, 'CCA': 1, 'UGG': 1})
#tests with arithmetic mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean),
0.75)
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=arithmetic_mean),
0.625)
ref_freqs_2 = cu.copy()
ref_freqs_2.update({'AGA': 4, 'AGG': 2, 'CCC': 5, 'CCA': 1, 'UGG': 1})
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_1(ref_freqs_2, gene_freqs, average=arithmetic_mean)
vals = [.8, .8, .8, .4, 1, 1, .2, .4, .2, .2]
expect = sum(vals) / len(vals)
self.assertFloatEqual(obs, expect)
#tests with geometric mean
gene_freqs = {'AGA': 1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGA': 5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGG': 5}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean),
0.5)
gene_freqs = {'AGG': 5, 'AGA': 5}
self.assertFloatEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.5**5)**(0.1))
gene_freqs = {'AGA': 5, 'CCC': 1}
self.assertEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean),
1)
gene_freqs = {'AGA': 5, 'CCA': 5}
self.assertFloatEqual(cai_1(ref_freqs, gene_freqs, average=geometric_mean), \
(1**5 * 0.25**5)**0.1)
ref_freqs_2 = cu.copy()
ref_freqs_2.update({'AGA': 4, 'AGG': 2, 'CCC': 5, 'CCA': 1, 'UGG': 1})
ref_freqs_2.update({'UUU': 2, 'UUC': 1})
gene_freqs = {
'AGA': 3,
'AGG': 1,
'CCC': 2,
'CCA': 1,
'UUU': 1,
'UUC': 2
}
obs = cai_1(ref_freqs_2, gene_freqs, average=geometric_mean)
vals = [.8, .8, .8, .4, 1, 1, .2, .4, .2, .2]
expect = (product(vals))**(1. / len(vals))
self.assertFloatEqual(obs, expect)
