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src/c/o/cogent-1.5.3/tests/test_maths/test_stats/test_cai/test_util.py   cogent(Download)
from math import log, exp
from operator import mul
from cogent.maths.stats.cai.util import cu, as_rna, synonyms_to_rna, \
    get_synonyms, sum_codon_freqs, norm_to_max, arithmetic_mean, \
    geometric_mean, codon_adaptiveness_all, codon_adaptiveness_blocks, \
        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)
        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)
        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)
            '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]]

src/p/y/pycogent-HEAD/tests/test_maths/test_stats/test_cai/test_util.py   pycogent(Download)
from math import log, exp
from operator import mul
from cogent.maths.stats.cai.util import cu, as_rna, synonyms_to_rna, \
    get_synonyms, sum_codon_freqs, norm_to_max, arithmetic_mean, \
    geometric_mean, codon_adaptiveness_all, codon_adaptiveness_blocks, \
        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)
        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)
        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)
            '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]]