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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, \
        - Single-codon blocs are M = 'AUG', W = 'UGG'
        """
        result = get_synonyms()
        self.assertEqual(len(result), 18)
        self.assertEqual(''.join(sorted(result)), 'ACDEFGHIKLNPQRSTVY')
        self.assertEqual(sorted(result['I']), ['AUA','AUC','AUU'])
 
        #check that we can do it without eliminating single-codon blocks
        result = get_synonyms(singles_removed=False)

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, \
        - Single-codon blocs are M = 'AUG', W = 'UGG'
        """
        result = get_synonyms()
        self.assertEqual(len(result), 18)
        self.assertEqual(''.join(sorted(result)), 'ACDEFGHIKLNPQRSTVY')
        self.assertEqual(sorted(result['I']), ['AUA','AUC','AUU'])
 
        #check that we can do it without eliminating single-codon blocks
        result = get_synonyms(singles_removed=False)