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):
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.')
try:
# New in scipy v0.11
from scipy.optimize import minimize
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='ML')
self.assertAlmostEqual(round(dN, 4), 0.0194, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0217, places=4)
except ImportError:
# TODO - Show a warning?
pass
from run_tests import is_numpy
try:
from math import lgamma # New in Python 2.7
except ImportError:
lgamma = None
if is_numpy() and lgamma:
class Test_MK(unittest.TestCase):
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)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
try:
# New in scipy v0.11
from scipy.optimize import minimize
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='ML')
self.assertAlmostEqual(round(dN, 4), 0.0194, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0217, places=4)
except ImportError:
# TODO - Show a warning?
pass
from run_tests import is_numpy
try:
from math import lgamma # New in Python 2.7
except ImportError:
lgamma = None
if is_numpy() and lgamma:
class Test_MK(unittest.TestCase):
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)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)