def load_jobs(self): appname = self.conf[self.confname]["_app"] # Only one Muscle job is necessary to run this task args = OrderedDict(self.args) args["-i"] = pjoin(GLOBALS["input_dir"], self.multiseq_file) args["-o"] = "alg.fasta" job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid]) job.cores = self.conf["threading"].get(appname, 1) job.add_input_file(self.multiseq_file) self.jobs.append(job)
def load_jobs(self): appname = self.conf[self.confname]["_app"] args = OrderedDict(self.args) # Mafft redirects resulting alg to std.output. The order of # arguments is important, input file must be the last # one. args[""] = pjoin(GLOBALS["input_dir"], self.multiseq_file) job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid]) job.add_input_file(self.multiseq_file) job.cores = self.conf["threading"][appname] self.jobs.append(job)
def load_jobs(self): args = self.args.copy() try: del args["-wag"] except KeyError: pass if self.constrain_tree: args["-constraints"] = pjoin(GLOBALS["input_dir"], self.constrain_tree) args[pjoin(GLOBALS["input_dir"], self.alg_phylip_file)] = "" appname = self.conf[self.confname]["_app"] job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid]) job.cores = self.conf["threading"][appname] if self.constrain_tree: job.add_input_file(self.constrain_tree) job.add_input_file(self.alg_phylip_file) self.jobs.append(job)
def load_jobs(self): args = OrderedDict(self.args) args["-s"] = pjoin(GLOBALS["input_dir"], self.alg_phylip_file) args["-m"] = self.model_string args["-n"] = self.alg_phylip_file if self.constrain_tree: log.log(24, "Using constrain tree %s" % self.constrain_tree) args["-g"] = pjoin(GLOBALS["input_dir"], self.constrain_tree) if self.partitions_file: log.log(24, "Using alg partitions %s" % self.partitions_file) args['-q'] = pjoin(GLOBALS["input_dir"], self.partitions_file) tree_job = Job(self.raxml_bin, args, parent_ids=[self.nodeid]) tree_job.jobname += "-" + self.model_string tree_job.cores = self.threads # Register input files necessary to run the job tree_job.add_input_file(self.alg_phylip_file) if self.constrain_tree: tree_job.add_input_file(self.constrain_tree) if self.partitions_file: tree_job.add_input_file(self.partitions_file) self.jobs.append(tree_job) self.out_tree_file = os.path.join( tree_job.jobdir, "RAxML_bestTree." + self.alg_phylip_file) if self.bootstrap == "alrt": alrt_args = tree_job.args.copy() if self.constrain_tree: del alrt_args["-g"] if self.partitions_file: alrt_args["-q"] = args['-q'] alrt_args["-f"] = "J" alrt_args["-t"] = self.out_tree_file alrt_job = Job(self.raxml_bin, alrt_args, parent_ids=[tree_job.jobid]) alrt_job.jobname += "-alrt" alrt_job.dependencies.add(tree_job) alrt_job.cores = self.threads # Register necessary input files alrt_job.add_input_file(self.alg_phylip_file) if self.partitions_file: alrt_job.add_input_file(self.partitions_file) self.jobs.append(alrt_job) self.alrt_job = alrt_job elif self.bootstrap == "alrt_phyml": alrt_args = { "-o": "n", "-i": self.alg_phylip_file, "--bootstrap": "-2", "-d": self.seqtype, "-u": self.out_tree_file, "--model": self.model, "--quiet": "", "--no_memory_check": "", } #if self.constrain_tree: # alrt_args["--constraint_tree"] = self.constrain_tree alrt_job = Job(self.conf["app"]["phyml"], alrt_args, parent_ids=[tree_job.jobid]) alrt_job.add_input_file(self.alg_phylip_file, alrt_job.jobdir) alrt_job.jobname += "-alrt" alrt_job.dependencies.add(tree_job) alrt_job.add_input_file(self.alg_phylip_file) self.jobs.append(alrt_job) self.alrt_job = alrt_job else: # Bootstrap calculation boot_args = tree_job.args.copy() boot_args["-n"] = "bootstraps." + boot_args["-n"] boot_args["-N"] = int(self.bootstrap) boot_args["-b"] = 31416 boot_job = Job(self.raxml_bin, boot_args, parent_ids=[tree_job.jobid]) boot_job.jobname += "-%d-bootstraps" % (boot_args['-N']) boot_job.dependencies.add(tree_job) boot_job.cores = self.threads # Register necessary input files boot_job.add_input_file(self.alg_phylip_file) if self.constrain_tree: boot_job.add_input_file(self.constrain_tree) if self.partitions_file: boot_job.add_input_file(self.partitions_file) self.jobs.append(boot_job) # Bootstrap drawing on top of best tree bootd_args = tree_job.args.copy() if self.constrain_tree: del bootd_args["-g"] if self.partitions_file: del bootd_args["-q"] bootd_args["-n"] = "bootstrapped." + tree_job.args["-n"] bootd_args["-f"] = "b" bootd_args["-t"] = self.out_tree_file bootd_args["-z"] = pjoin(boot_job.jobdir, "RAxML_bootstrap." + boot_job.args["-n"]) bootd_job = Job(self.raxml_bin, bootd_args, parent_ids=[tree_job.jobid]) bootd_job.jobname += "-bootstrapped" bootd_job.dependencies.add(boot_job) bootd_job.cores = self.threads self.jobs.append(bootd_job) self.boot_job = boot_job self.bootd_job = bootd_job
def load_jobs(self): args = OrderedDict(self.args) args["-s"] = pjoin(GLOBALS["input_dir"], self.alg_phylip_file) args["-m"] = self.model_string args["-n"] = self.alg_phylip_file if self.constrain_tree: log.log(24, "Using constrain tree %s" %self.constrain_tree) args["-g"] = pjoin(GLOBALS["input_dir"], self.constrain_tree) if self.partitions_file: log.log(24, "Using alg partitions %s" %self.partitions_file) args['-q'] = pjoin(GLOBALS["input_dir"], self.partitions_file) tree_job = Job(self.raxml_bin, args, parent_ids=[self.nodeid]) tree_job.jobname += "-"+self.model_string tree_job.cores = self.threads # Register input files necessary to run the job tree_job.add_input_file(self.alg_phylip_file) if self.constrain_tree: tree_job.add_input_file(self.constrain_tree) if self.partitions_file: tree_job.add_input_file(self.partitions_file) self.jobs.append(tree_job) self.out_tree_file = os.path.join(tree_job.jobdir, "RAxML_bestTree." + self.alg_phylip_file) if self.bootstrap == "alrt": alrt_args = tree_job.args.copy() if self.constrain_tree: del alrt_args["-g"] if self.partitions_file: alrt_args["-q"] = args['-q'] alrt_args["-f"] = "J" alrt_args["-t"] = self.out_tree_file alrt_job = Job(self.raxml_bin, alrt_args, parent_ids=[tree_job.jobid]) alrt_job.jobname += "-alrt" alrt_job.dependencies.add(tree_job) alrt_job.cores = self.threads # Register necessary input files alrt_job.add_input_file(self.alg_phylip_file) if self.partitions_file: alrt_job.add_input_file(self.partitions_file) self.jobs.append(alrt_job) self.alrt_job = alrt_job elif self.bootstrap == "alrt_phyml": alrt_args = { "-o": "n", "-i": self.alg_phylip_file, "--bootstrap": "-2", "-d": self.seqtype, "-u": self.out_tree_file, "--model": self.model, "--quiet": "", "--no_memory_check": "", } #if self.constrain_tree: # alrt_args["--constraint_tree"] = self.constrain_tree alrt_job = Job(self.conf["app"]["phyml"], alrt_args, parent_ids=[tree_job.jobid]) alrt_job.add_input_file(self.alg_phylip_file, alrt_job.jobdir) alrt_job.jobname += "-alrt" alrt_job.dependencies.add(tree_job) alrt_job.add_input_file(self.alg_phylip_file) self.jobs.append(alrt_job) self.alrt_job = alrt_job else: # Bootstrap calculation boot_args = tree_job.args.copy() boot_args["-n"] = "bootstraps."+boot_args["-n"] boot_args["-N"] = int(self.bootstrap) boot_args["-b"] = 31416 boot_job = Job(self.raxml_bin, boot_args, parent_ids=[tree_job.jobid]) boot_job.jobname += "-%d-bootstraps" %(boot_args['-N']) boot_job.dependencies.add(tree_job) boot_job.cores = self.threads # Register necessary input files boot_job.add_input_file(self.alg_phylip_file) if self.constrain_tree: boot_job.add_input_file(self.constrain_tree) if self.partitions_file: boot_job.add_input_file(self.partitions_file) self.jobs.append(boot_job) # Bootstrap drawing on top of best tree bootd_args = tree_job.args.copy() if self.constrain_tree: del bootd_args["-g"] if self.partitions_file: del bootd_args["-q"] bootd_args["-n"] = "bootstrapped."+ tree_job.args["-n"] bootd_args["-f"] = "b" bootd_args["-t"] = self.out_tree_file bootd_args["-z"] = pjoin(boot_job.jobdir, "RAxML_bootstrap." + boot_job.args["-n"]) bootd_job = Job(self.raxml_bin, bootd_args, parent_ids=[tree_job.jobid]) bootd_job.jobname += "-bootstrapped" bootd_job.dependencies.add(boot_job) bootd_job.cores = self.threads self.jobs.append(bootd_job) self.boot_job = boot_job self.bootd_job = bootd_job