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src/b/i/biopython-HEAD/Tests/test_CodonAlign.py   biopython(Download)
                with warnings.catch_warnings():
                    warnings.simplefilter('ignore')
                    caln = CodonAlign.build(prot, nucl, alphabet=CodonAlign.default_codon_alphabet)
            elif i[1] == 'index':
                nucl = SeqIO.index(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
                prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
                with warnings.catch_warnings():
                    warnings.simplefilter('ignore')
                    caln = CodonAlign.build(prot, nucl, alphabet=CodonAlign.default_codon_alphabet, max_score=20)
                with warnings.catch_warnings():
                    warnings.simplefilter('ignore')
                    caln = CodonAlign.build(prot, nucl, corr_dict=id, alphabet=CodonAlign.default_codon_alphabet)
            alns.append(caln)
            nucl.close() # Close the indexed FASTA file
    def test_build(self):
        codon_aln1 = CodonAlign.build(self.aln1, self.seqlist1)
        codon_aln2 = CodonAlign.build(self.aln2, self.seqlist2)
 
class Test_dn_ds(unittest.TestCase):