def test_mk(self): p = SeqIO.index(TEST_ALIGN_FILE7[0][0], "fasta") pro_aln = AlignIO.read(TEST_ALIGN_FILE7[0][1], "clustal") codon_aln = codonalign.build(pro_aln, p) p.close() # Close indexed FASTA file self.assertAlmostEqual(codonalign.mktest( [codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]), 0.0021, places=4)
def test_mk(self): p = SeqIO.index(TEST_ALIGN_FILE7[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA()) pro_aln = AlignIO.read(TEST_ALIGN_FILE7[0][1], 'clustal', alphabet=IUPAC.protein) codon_aln = codonalign.build(pro_aln, p) p.close() # Close indexed FASTA file self.assertAlmostEqual(codonalign.mktest( [codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]), 0.0021, places=4)
def test_mk(self): p = SeqIO.index(TEST_ALIGN_FILE7[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA()) pro_aln = AlignIO.read(TEST_ALIGN_FILE7[0][1], 'clustal', alphabet=IUPAC.protein) codon_aln = codonalign.build(pro_aln, p) p.close() # Close indexed FASTA file self.assertAlmostEqual(round(codonalign.mktest([codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]), 4), 0.0021, places=4)