def finish(self):
# first job is the raxml tree
best_model = None
best_model_in_next_line = False
t = None
for line in open(self.jobs[-1].stdout_file, "rU"):
line = line.strip()
if best_model_in_next_line and line.startswith("Model"):
pass#best_model = line.split("=")[1].strip()
elif best_model_in_next_line and line.startswith("partition"):
best_model = line.split("=")[1].strip()
best_model_in_next_line = False
elif line.startswith("Model selected:"):
best_model_in_next_line = True
elif line.startswith("ML tree (NNI) for the best AIC model ="):
nw = line.replace("ML tree (NNI) for the best AIC model =", "")
t = PhyloTree(nw)
open(self.best_model_file, "w").write(best_model)
log.log(26, "Best model: %s" %best_model)
if self.ttype == "tree":
tree_job = self.jobs[-1]
tree_file = os.path.join(tree_job.jobdir,
"jModelTest_tree."+self.nodeid)
t.write(outfile=self.tree_file)
self.model = best_model
ModelTesterTask.finish(self)
def finish(self):
lks = []
if self.lk_mode == "phyml":
for job in [j for j in self.jobs if j.flag == "phyml"]:
tree_file = os.path.join(job.jobdir,
self.alg_basename+"_phyml_tree.txt")
stats_file = os.path.join(j.jobdir,
self.alg_basename+"_phyml_stats.txt")
tree = PhyloTree(tree_file)
m = re.search('Log-likelihood:\s+(-?\d+\.\d+)',
open(stats_file).read())
lk = float(m.groups()[0])
tree.add_feature("lk", lk)
tree.add_feature("model", job.args["--model"])
lks.append([float(tree.lk), tree.model, tree])
elif self.lk_mode == "raxml":
for job in [j for j in self.jobs if j.flag == "raxml"]:
lk = open(os.path.join(job.jobdir, "RAxML_log.%s"
%job.args["-n"])).readline().split()[1]
tree = PhyloTree(job.args["-t"])
tree.add_feature("lk", lk)
tree.add_feature("model", job.model)
lks.append([lk, tree.model, tree])
lks.sort()
lks.reverse()
# choose the model with higher likelihood
best_model = lks[-1][1]
best_tree = lks[-1][2]
open(self.best_model_file, "w").write(best_model)
if self.tree_file:
tree.write(self.tree_file)
ModelTesterTask.finish(self)
def finish(self):
lks = []
j = self.jobs[0]
tree_file = os.path.join(j.jobdir,
self.alg_phylip_file+"_phyml_tree.txt")
stats_file = os.path.join(j.jobdir,
self.alg_phylip_file+"_phyml_stats.txt")
m = re.search('Log-likelihood:\s+(-?\d+\.\d+)',
open(stats_file).read())
lk = float(m.groups()[0])
stats = {"lk": lk}
tree = PhyloTree(tree_file)
TreeTask.store_data(self, tree.write(), stats)
