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)
def finish(self):
node_info = self.conf["_nodeinfo"][self.nodeid]
target_seqs = node_info.get("target_seqs", set())
out_seqs = node_info.get("out_seqs", set())
all_seqs = list(target_seqs | out_seqs)
if len(all_seqs) == 1:
newick = "%s;" %(all_seqs[0])
elif len(all_seqs) == 2:
newick = "(%s, %s);" %(all_seqs[0], all_seqs[1])
else:
newick = "(%s, (%s));" %(all_seqs[0], ','.join(all_seqs[1:]))
TreeTask.store_data(self, newick, {})
def finish(self):
#first job is the raxml tree
def parse_alrt(match):
dist = match.groups()[0]
support = float(match.groups()[1])/100.0
return "%g:%s" %(support, dist)
if self.bootstrap == "alrt":
alrt_tree_file = os.path.join(self.alrt_job.jobdir,
"RAxML_fastTreeSH_Support." + self.alrt_job.args["-n"])
raw_nw = open(alrt_tree_file).read()
try:
nw, nsubs = re.subn(":(\d+\.\d+)\[(\d+)\]", parse_alrt, raw_nw, flags=re.MULTILINE)
except TypeError:
raw_nw = raw_nw.replace("\n","")
nw, nsubs = re.subn(":(\d+\.\d+)\[(\d+)\]", parse_alrt, raw_nw)
if nsubs == 0:
log.warning("alrt values were not detected in raxml tree!")
tree = Tree(nw)
elif self.bootstrap == "alrt_phyml":
alrt_tree_file = os.path.join(self.alrt_job.jobdir,
self.alg_phylip_file +"_phyml_tree.txt")
tree = Tree(alrt_tree_file)
else:
alrt_tree_file = os.path.join(self.bootd_job.jobdir,
"RAxML_bipartitions." + self.bootd_job.args["-n"])
nw = open(alrt_tree_file).read()
tree = Tree(nw)
tree.support = 100
for n in tree.traverse():
if n.support >1:
n.support /= 100.
else:
n.support = 0
TreeTask.store_data(self, tree.write(), {})
def finish(self):
job = self.jobs[-1]
t = Tree(job.stdout_file)
TreeTask.store_data(self, t.write(), {})
