def optimize_model(self, gtree, aln):
"""Optimizes the IQTREE model"""
fd, btreefile = tempfile.mkstemp('.btree')
os.close(fd)
gtree.write(btreefile)
fd, seqfile = tempfile.mkstemp('.align')
os.close(fd)
out = util.open_stream(seqfile, "w")
phylip.write_phylip_align(out, aln, strip_names=False)
out.close()
self.seqfile = seqfile
fd, bsitelhfile = tempfile.mkstemp('.bsitelh')
os.close(fd)
os.system('iqtree-omp -redo -nt %s -m %s -st %s -s %s -te %s -pre %s.treefix_tmp -wsl > /dev/null' % (self.cpu, self.model, self.type, self.seqfile, btreefile, self.pre))
f = open("%s.treefix_tmp.sitelh" % self.pre, 'r')
self.bsitelh = f.readline().replace("1", "2", 1) + f.readline().replace("Site_Lh", "Tree1", 1)
f.close()
os.system('rm %s.treefix_tmp.*' % self.pre)
os.remove(btreefile)
def optimize_model(self, gtree, aln):
"""Optimizes the IQTREE model"""
fd, btreefile = tempfile.mkstemp('.btree')
os.close(fd)
gtree.write(btreefile)
self.btreefile = btreefile
fd, seqfile = tempfile.mkstemp('.align')
os.close(fd)
out = util.open_stream(seqfile, "w")
phylip.write_phylip_align(out, aln, strip_names=False)
out.close()
self.seqfile = seqfile
def optimize_model(self, gtree, aln):
"""Optimizes the RAxML model"""
StatModel.optimize_model(self, gtree, aln)
fd, treefile = tempfile.mkstemp('.tree')
os.close(fd)
gtree.write(treefile)
fd, seqfile = tempfile.mkstemp('.align')
os.close(fd)
out = util.open_stream(seqfile, "w")
phylip.write_phylip_align(out, aln, strip_names=False)
out.close()
self._raxml.optimize_model(treefile, seqfile,
"-m %s -e %s -n test" % (self.model, self.eps))
os.remove(treefile)
os.remove(seqfile)
def optimize_model(self, gtree, aln):
"""Optimizes the IQTREE model"""
fd, btreefile = tempfile.mkstemp('.btree')
os.close(fd)
gtree.write(btreefile)
self.btreefile = btreefile
fd, seqfile = tempfile.mkstemp('.align')
os.close(fd)
out = util.open_stream(seqfile, "w")
phylip.write_phylip_align(out, aln, strip_names=False)
out.close()
self.seqfile = seqfile
# optimize all model parameters and create a model file for DNA data, or optimize the gamma shape parameter for other data type if necessary
if self.type == "DNA" or "+G" in self.model:
# optimize model parameters on user specified tree
os.system('iqtree-omp -redo -nt %s -m %s -st %s -s %s -te %s -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.model, self.type, self.seqfile, self.btreefile, self.pre))
# DNA data
if self.type == "DNA":
# create model file for DNA data
fd, modelfile = tempfile.mkstemp('.model')
os.close(fd)
self.modelfile = modelfile
# read estimated model parameters from IQTREE output
fi = open("%s.treefix_tmp.iqtree" % self.pre, 'r')
fo = open(modelfile, 'w')
line = fi.readline()
while line:
if "Rate parameter R:" in line:
fi.readline()
while True:
line = fi.readline().rstrip()
if ":" in line or "=" in line:
param = re.split('\s+', line)
fo.write("%s\n" % param[-1])
else:
break
elif "State frequencies:" in line:
if "equal frequencies" in line:
for i in range(4):
fo.write("0.25\n")
else:
fi.readline()
while True:
line = fi.readline().rstrip()
if ":" in line or "=" in line:
param = re.split('\s+', line)
fo.write("%s\n" % param[-1])
else:
break
elif "Gamma shape alpha:" in line:
param = re.split('\s+', line)
self.gamma = param[3]
break
line = fi.readline()
fi.close()
fo.close()
# set command for stats
if "+G" in self.model:
if self.test == "AU":
self.cmd = 'iqtree-omp -redo -nt %s -m %s+G+Fu -a %s -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -au -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.modelfile, self.gamma, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
else:
self.cmd = 'iqtree-omp -redo -nt %s -m %s+G+Fu -a %s -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.modelfile, self.gamma, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
else:
if self.test == "AU":
self.cmd = 'iqtree-omp -redo -nt %s -m %s+Fu -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -au -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.modelfile, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
else:
self.cmd = 'iqtree-omp -redo -nt %s -m %s+Fu -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.modelfile, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
# other data type
elif "+G" in self.model:
# read estimated model parameters from IQTREE outptut
fi = open("%s.treefix_tmp.iqtree" % self.pre, 'r')
for line in fi:
if "Gamma shape alpha:" in line:
param = re.split('\s+', line)
self.gamma = param[3]
break
fi.close()
# set command for stats
if self.test == "AU":
self.cmd = 'iqtree-omp -redo -nt %s -m %s -a %s -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -au -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.model, self.gamma, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
else:
self.cmd = 'iqtree-omp -redo -nt %s -m %s -a %s -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.model, self.gamma, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
# clean up files generated during model optimization
os.system('rm %s.treefix_tmp.*' % self.pre)
else:
# set command for stats
if self.test == "AU":
self.cmd = 'iqtree-omp -redo -nt %s -m %s -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -au -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.model, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
else:
self.cmd = 'iqtree-omp -redo -nt %s -m %s -st %s -s %s -te %s -z %s.treefix_tmp.tree -zb %s -pre %s.treefix_tmp > /dev/null' % (self.cpu, self.model, self.type, self.seqfile, self.btreefile, self.pre, self.rep, self.pre)
