예제 #1
0
파일: prottest2.py 프로젝트: a1an77/ete
    def load_jobs(self):
        for m in self.models:
            args = self.args.copy()
            args["--model"] = m
            job = Job(self.conf["app"]["phyml"], args,
                      parent_ids=[self.nodeid], jobname="phyml-bionj")
            job.flag = "phyml"
            self.jobs.append(job)

            if self.lk_mode == "raxml":
                raxml_args = {
                    "-f": "e", 
                    "-s": self.alg_basename,
                    "-m": "PROTGAMMA%s" % m,
                    "-n": self.alg_basename+"."+m,
                    "-t": os.path.join(GLOBALS["tasks_dir"], job.jobid,
                                       self.alg_basename+"_phyml_tree.txt")
                    }
                raxml_job = Job(self.conf["app"]["raxml"], raxml_args,
                                parent_ids=[job.jobid], jobname="raxml-tree-optimize")
                raxml_job.dependencies.add(job)
                raxml_job.flag = "raxml"
                raxml_job.model = m
                self.jobs.append(raxml_job)
            
        log.log(26, "Models to test %s", self.models)
예제 #2
0
파일: prottest.py 프로젝트: F4L2/devoirs
    def load_jobs(self):
        conf = self.conf
        for m in self.models:
            args = self.args.copy()
            args["--model"] = m
            bionj_job = Job(conf["app"]["phyml"], args,
                      parent_ids=[self.nodeid])
            bionj_job.jobname += "-bionj-" + m
            bionj_job.jobcat = "bionj"
            bionj_job.add_input_file(self.alg_phylip_file, bionj_job.jobdir)
            self.jobs.append(bionj_job)

            if self.lk_mode == "raxml":
                raxml_args = {
                    "-f": "e", 
                    "-s": pjoin(bionj_job.jobdir, self.alg_phylip_file),
                    "-m": "PROTGAMMA%s" % m,
                    "-n": self.alg_phylip_file+"."+m,
                    "-t": pjoin(bionj_job.jobdir,
                                       self.alg_phylip_file+"_phyml_tree.txt")
                    }
                raxml_job = Job(conf["app"]["raxml"], raxml_args,
                                parent_ids=[bionj_job.jobid])
                raxml_job.jobname += "-lk-optimize"
                raxml_job.dependencies.add(bionj_job)
                raxml_job.model = m
                raxml_job.jobcat = "raxml"
                self.jobs.append(raxml_job)
예제 #3
0
파일: prottest2.py 프로젝트: F4L2/devoirs
    def load_jobs(self):
        for m in self.models:
            args = self.args.copy()
            args["--model"] = m
            job = Job(self.conf["app"]["phyml"],
                      args,
                      parent_ids=[self.nodeid],
                      jobname="phyml-bionj")
            job.flag = "phyml"
            self.jobs.append(job)

            if self.lk_mode == "raxml":
                raxml_args = {
                    "-f":
                    "e",
                    "-s":
                    self.alg_basename,
                    "-m":
                    "PROTGAMMA%s" % m,
                    "-n":
                    self.alg_basename + "." + m,
                    "-t":
                    os.path.join(GLOBALS["tasks_dir"], job.jobid,
                                 self.alg_basename + "_phyml_tree.txt")
                }
                raxml_job = Job(self.conf["app"]["raxml"],
                                raxml_args,
                                parent_ids=[job.jobid],
                                jobname="raxml-tree-optimize")
                raxml_job.dependencies.add(job)
                raxml_job.flag = "raxml"
                raxml_job.model = m
                self.jobs.append(raxml_job)

        log.log(26, "Models to test %s", self.models)