def test_mk(self): ver = sys.version_info if ver[0] == 2 and ver[1] == 6: warnings.warn('Python 2.6 detected. Skip testing MK method') pass else: from run_tests import is_numpy if is_numpy(): 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) self.assertAlmostEquals(round(CodonAlign.mktest([codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]), 4), 0.0021, places=4) else: warnings.warn('Numpy not installed. Skip MK test.')
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)
def test_mk(self): ver = sys.version_info if ver[0] == 2 and ver[1] == 6: warnings.warn('Python 2.6 detected. Skip testing MK method') pass else: from run_tests import is_numpy if is_numpy(): 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) self.assertAlmostEquals(round( CodonAlign.mktest( [codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]), 4), 0.0021, places=4) else: warnings.warn('Numpy not installed. Skip MK test.')
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)