def setUp(self): self.aln_file = [TEST_ALIGN_FILE1, TEST_ALIGN_FILE2, TEST_ALIGN_FILE3, TEST_ALIGN_FILE4, TEST_ALIGN_FILE5, TEST_ALIGN_FILE6] alns = [] for i in self.aln_file: if i[1] == 'parse': nucl = SeqIO.parse(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) 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) elif i[1] == 'id': nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA()) prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein) with open(i[0][2]) as handle: id = dict((i.split()[0], i.split()[1]) for i in handle) 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 self.alns = alns
def setUp(self): nucl = SeqIO.parse(TEST_ALIGN_FILE6[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA()) prot = AlignIO.read(TEST_ALIGN_FILE6[0][1], 'clustal', alphabet=IUPAC.protein) with open(TEST_ALIGN_FILE6[0][2]) as handle: id_corr = dict((i.split()[0], i.split()[1]) for i in handle) aln = CodonAlign.build(prot, nucl, corr_dict=id_corr, alphabet=CodonAlign.default_codon_alphabet) self.aln = aln
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_build(self): codon_aln1 = CodonAlign.build(self.aln1, self.seqlist1) codon_aln2 = CodonAlign.build(self.aln2, self.seqlist2)
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)