def load_jobs(self): # Only one Muscle job is necessary to run this task appname = self.conf[self.confname]["_app"] args = OrderedDict(self.args) args["-in"] = pjoin(GLOBALS["input_dir"], self.multiseq_file) args["-out"] = "alg.fasta" job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid]) 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 __init__(self, nodeid, multiseq_file, seqtype, conf, confname): GLOBALS["citator"].add(MAFFT_CITE) self.confname = confname self.conf = conf # Initialize task AlgTask.__init__(self, nodeid, "alg", "Mafft", OrderedDict(), self.conf[confname]) self.seqtype = seqtype self.multiseq_file = multiseq_file self.init()
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname): self.confname = confname self.conf = conf # Initialize task AlgTask.__init__(self, nodeid, "alg", "Meta-Alg", OrderedDict(), self.conf[self.confname]) self.seqtype = seqtype self.multiseq_file = multiseq_file self.size = conf["_nodeinfo"][nodeid].get("size", 0) self.all_alg_files = None self.init()
def __init__(self, nodeid, multiseq_file, seqtype, conf): # Initialize task AlgTask.__init__(self, nodeid, "alg", "Usearch-Uhire", OrderedDict(), conf["uhire"]) self.conf = conf self.seqtype = seqtype self.multiseq_file = multiseq_file self.init() self.alg_fasta_file = os.path.join(self.taskdir, "final_alg.fasta") self.alg_phylip_file = os.path.join(self.taskdir, "final_alg.iphylip")
def __init__(self, nodeid, seqtype, all_alg_files, conf, confname, parent_ids): GLOBALS["citator"].add(MCOFFEE_CITE) base_args = OrderedDict({ "-output": "fasta", }) # Initialize task self.confname = confname self.conf = conf AlgTask.__init__(self, nodeid, "alg", "Mcoffee", base_args, self.conf[confname]) self.all_alg_files = all_alg_files self.parent_ids = parent_ids self.seqtype = seqtype self.init()
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname): GLOBALS["citator"].add(DIALIGN_CITE) # fixed options for running this task base_args = OrderedDict({ '': None, }) # Initialize task self.confname = confname self.conf = conf AlgTask.__init__(self, nodeid, "alg", "DialignTX", base_args, self.conf[self.confname]) self.seqtype = seqtype self.multiseq_file = multiseq_file self.init()
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname): GLOBALS["citator"].add(MUSCLE_CITE) # fixed Muscle options base_args = OrderedDict({ '-in': None, '-out': None, }) self.confname = confname self.conf = conf # Initialize task AlgTask.__init__(self, nodeid, "alg", "Muscle", base_args, self.conf[confname]) self.seqtype = seqtype self.multiseq_file = multiseq_file self.init()
def load_jobs(self): appname = self.conf[self.confname]["_app"] args = OrderedDict(self.args) args["--model"] = self.model args["--datatype"] = self.seqtype args["--input"] = self.alg_phylip_file if self.constrain_tree: args["--constraint_tree"] = self.constrain_tree args["-u"] = self.constrain_tree else: del args["--constraint_tree"] job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid]) job.add_input_file(self.alg_phylip_file, job.jobdir) if self.constrain_tree: job.add_input_file(self.constrain_tree, job.jobdir) job.jobname += "-" + self.model self.jobs.append(job)
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname): GLOBALS["citator"].add(CLUSTALO_CITE) base_args = OrderedDict({ '-i': None, '-o': None, '--outfmt': "fa", }) self.confname = confname self.conf = conf # Initialize task AlgTask.__init__(self, nodeid, "alg", "Clustal-Omega", base_args, self.conf[self.confname]) self.seqtype = seqtype self.multiseq_file = multiseq_file self.init()
def __init__(self, nodeid, alg_file, constrain_id, model, seqtype, conf, confname, parts_id=None): GLOBALS["citator"].add(FASTTREE_CITE) self.confname = confname self.conf = conf self.alg_phylip_file = alg_file self.constrain_tree = None if constrain_id: self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_alg) self.alg_basename = basename(self.alg_phylip_file) self.seqtype = seqtype self.tree_file = "" if model: log.warning("FastTree does not support model selection") self.model = None self.lk = None base_args = OrderedDict() base_args["-nopr"] = "" if self.seqtype == "nt": base_args["-gtr -nt"] = "" elif self.seqtype == "aa": pass else: raise ValueError("Unknown seqtype %s" % self.seqtype) TreeTask.__init__(self, nodeid, "tree", "FastTree", base_args, self.conf[confname]) self.init()
def __init__(self, nodeid, alg_phylip_file, constrain_id, model, seqtype, conf, confname, parts_id=None): GLOBALS["citator"].add(PHYML_CITE) base_args = OrderedDict({ "--model": "", "--no_memory_check": "", "--quiet": "", "--constraint_tree": "" }) self.confname = confname self.conf = conf self.constrain_tree = None if constrain_id: self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_tree) self.alg_phylip_file = alg_phylip_file TreeTask.__init__(self, nodeid, "tree", "Phyml", base_args, conf[confname]) if seqtype == "aa": self.model = model or conf[confname]["_aa_model"] elif seqtype == "nt": self.model = model or conf[confname]["_nt_model"] self.seqtype = seqtype self.lk = None self.init()
def __init__(self, nodeid, alg_file, constrain_id, model, seqtype, conf, confname, parts_id=None): GLOBALS["citator"].add(RAXML_CITE) base_args = OrderedDict() self.bootstrap = conf[confname].get("_bootstrap", None) model = model or conf[confname]["_aa_model"] self.confname = confname self.conf = conf self.alg_phylip_file = alg_file try: self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_tree) except ValueError: self.constrain_tree = None self.partitions_file = parts_id TreeTask.__init__(self, nodeid, "tree", "RaxML", base_args, conf[confname]) max_cores = GLOBALS["_max_cores"] appname = conf[confname]["_app"] if max_cores > 1: threads = conf["threading"].get("raxml-pthreads") if threads > 1: appname = appname.replace("raxml", "raxml-pthreads") raxml_bin = conf["app"][appname] else: appname = appname.replace("raxml-pthreads", "raxml") threads = 1 raxml_bin = conf["app"][appname] self.raxml_bin = raxml_bin self.threads = threads self.seqtype = seqtype # Process raxml options method = conf[confname].get("_method", "GAMMA").upper() if seqtype.lower() == "aa": self.model_string = 'PROT%s%s' % (method, model.upper()) self.model = model elif seqtype.lower() == "nt": self.model_string = 'GTR%s' % method self.model = "GTR" else: raise ValueError("Unknown seqtype %s", seqtype) #inv = conf[confname].get("pinv", "").upper() #freq = conf[confname].get("ebf", "").upper() self.init()
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