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)
