def test_iqtree_outfile(self):
out = os.path.join(PATH, 'tests', 'data', 'mlt',
'iqtree.ml.tree.newick')
outfile = mlt(IQTREE, self.msa, outfile=out)
self.assertTrue(os.path.isfile(outfile))
self.assertEqual(out, outfile)
self.assertTrue(_newick(out))
self.rm = out
def test_phyml_outfile(self):
out = os.path.join(PATH, 'tests', 'data', 'mlt',
'phyml.ml.tree.newick')
outfile = mlt(PHYML, self.msa, outfile=out)
self.assertTrue(os.path.isfile(outfile))
self.assertEqual(out, outfile)
self.assertTrue(_newick(out))
self.rm = out
def _iqtree(exe, msa, tree, model, seed):
"""
Perform topology test (AU test) using IQ-TREE_.
:param msa: str, path to a FASTA format MSA file.
:param tree: str, path to a NEWICK format tree file.
:param exe: str, path to a topology test program's executable.
:param model: str, name of the model or path of the model file.
:param seed: int, the seed used to initiate the random number generator.
:return: tuple, p-value of the AU test (float), first tree (string), and
second tree (string).
.. _IQ-TREE: www.iqtree.org/
"""
trees = Phylo.parse(tree, 'newick')
number = sum(1 for t in trees)
wd = tempfile.mkdtemp(dir=os.path.dirname(os.path.abspath(msa)))
args = [
exe, '-s', 'msa.fasta', '-zb', '10000', '-au', '-nt', '1', '-pre',
'autest', '-n', '0'
]
if model:
args.extend(['-m', model])
else:
args.extend(['-m', 'TEST'])
shutil.copy(msa, os.path.join(wd, 'msa.fasta'))
t1, t2 = '', ''
if number == 1:
info('One tree found in tree file, inferring ML tree.')
mltree = mlt(exe, msa, model=model)
if mltree:
trees = os.path.join(wd, 'trees.newick')
if isinstance(tree, str):
with open(tree) as f1:
t1 = f1.readline().rstrip()
else:
t1 = tree.format('newick').rstrip()
with open(trees, 'w') as o, open(mltree) as f2:
t2 = f2.read().strip()
o.write('{}\n{}\n'.format(t1, t2))
args.extend(['-z', 'trees.newick'])
else:
error('Infer ML tree failed, AU TEST aborted.')
sys.exit(1)
else:
with open(tree) as f:
t1, t2 = f.readline().strip(), f.readline().strip()
shutil.copy(tree, os.path.join(wd, 'trees.newick'))
args.extend(['-z', 'trees.newick'])
try:
info('Running AU TEST (IQ-TREE) using the following command:\n\t'
'{}'.format(' '.join(args)))
process = Popen(args,
cwd=wd,
stdout=PIPE,
stderr=PIPE,
universal_newlines=True)
code = process.wait()
if code:
msg = indent(process.stderr.read(), prefix='\t')
error('Topology test (AU TEST) failed for {}\n{}'.format(msa, msg))
sys.exit(1)
else:
info('Parsing tree topology test (AU TEST) results.')
with open(os.path.join(wd, 'autest.iqtree')) as f:
for line in f:
if 'USER TREES' in line:
break
for line in f:
if line.strip().startswith('1'):
aup = float(line.split()[-2])
return aup, t1, t2
error('Parsing tree topology test (AU TEST) failed, no test'
'result found.')
sys.exit(1)
except OSError:
error('Invalid IQ-TREE executable (exe) {}, topology test (AU TEST) '
'failed for {}.'.format(exe, msa))
sys.exit(1)
finally:
shutil.rmtree(wd)
def test_raxml_dfault(self):
out = mlt(RAXML, self.msa)
self.assertTrue(os.path.isfile(out))
self.assertTrue(_newick(out))
self.rm = out
def test_iqtree_dfault(self):
out = mlt(IQTREE, self.msa)
self.assertTrue(os.path.isfile(out))
self.assertTrue(_newick(out))
self.rm = out