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) newick = "(%s, (%s));" %(all_seqs[0], ','.join(all_seqs[1:])) TreeTask.store_data(self, newick, {})
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) newick = "(%s, (%s));" % (all_seqs[0], ','.join(all_seqs[1:])) TreeTask.store_data(self, newick, {})
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): 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): #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): #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(), {})
def finish(self): job = self.jobs[-1] t = Tree(job.stdout_file) TreeTask.store_data(self, t.write(), {})