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src/b/i/biopython-HEAD/Bio/CodonAlign/CodonAlignment.py   biopython(Download)
 
from Bio.CodonAlign.CodonAlphabet import default_codon_table, default_codon_alphabet
from Bio.CodonAlign.CodonSeq import _get_codon_list, CodonSeq, cal_dn_ds
from Bio.CodonAlign.chisq import chisqprob
 
            for j in range(i+1):
                if i != j:
                    dn, ds = cal_dn_ds(self._records[i], self._records[j],
                                       method=method)
                    dn_matrix[i].append(dn)

src/b/i/biopython-HEAD/Tests/test_CodonAlign.py   biopython(Download)
    def test_dn_ds(self):
        from Bio.CodonAlign.CodonSeq import cal_dn_ds
        codon_seq1 = self.aln[0]
        codon_seq2 = self.aln[1]
        dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='NG86')
        self.assertAlmostEqual(round(dN, 4), 0.0209, places=4)
        self.assertAlmostEqual(round(dS, 4), 0.0178, places=4)
        dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='LWL85')
        # This should be present:
        from scipy.linalg import expm
        dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='YN00')
        self.assertAlmostEqual(round(dN, 4), 0.0198, places=4)
        self.assertAlmostEqual(round(dS, 4), 0.0222, places=4)
 
        try:
            # New in scipy v0.11
            from scipy.optimize import minimize
            dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='ML')