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src/p/y/pycogent-HEAD/tests/test_maths/test_stats/test_cai/test_util.py   pycogent(Download)
    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':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})
        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})
    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
        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})

src/c/o/cogent-1.5.3/tests/test_maths/test_stats/test_cai/test_util.py   cogent(Download)
    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':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})
        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})
    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
        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})