def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, constrain_tree, conf, confname): GLOBALS["citator"].add(PHYML_CITE) self.alg_phylip_file = alg_phylip_file self.alg_fasta_file = alg_fasta_file self.confname = confname self.conf = conf self.lk_mode = conf[confname]["_lk_mode"] if self.lk_mode == "raxml": phyml_optimization = "n" elif self.lk_mode == "phyml": phyml_optimization = "lr" else: raise ValueError("Choose a valid lk_mode value (raxml or phyml)") base_args = { "--datatype": "aa", "--input": self.alg_phylip_file, "--bootstrap": "0", "-o": phyml_optimization, "--model": None, # I will iterate over this value when # creating jobs "--quiet": "" } self.models = conf[confname]["_models"] task_name = "Prottest-[%s]" %','.join(self.models) ModelTesterTask.__init__(self, nodeid, "mchooser", task_name, base_args, conf[confname]) self.best_model = None self.seqtype = "aa" self.init()
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, conf): GLOBALS["citator"].add(JMODELTEST_CITE) self.conf = conf base_args = { '-d': alg_fasta_file, } args = self.conf["jmodeltest"] if args.get("-t", "ML") == "ML": task_type = "tree" else: task_type = "mchooser" ModelTesterTask.__init__(self, nodeid, task_type, "Jmodeltest", base_args, self.conf[confname]) # set app arguments and options self.alg_fasta_file = alg_fasta_file self.alg_phylip_file = alg_phylip_file self.seqtype = "nt" self.models = "see jmodeltest params" self.init() self.best_model_file = os.path.join(self.taskdir, "best_model.txt") if task_type == "tree": self.tree_file = os.path.join(self.taskdir, "final_tree.nw") else: self.tree_file = None
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, constrain_tree, conf): self.alg_phylip_file = alg_phylip_file self.alg_fasta_file = alg_fasta_file self.alg_basename = basename(self.alg_phylip_file) self.conf = conf self.lk_mode = self.conf["prottest"]["_lk_mode"] if self.lk_mode == "raxml": phyml_optimization = "n" elif self.lk_mode == "phyml": phyml_optimization = "lr" else: raise ValueError("Choose a valid lk_mode value (raxml or phyml)") base_args = { "--datatype": "aa", "--input": self.alg_basename, "--bootstrap": "0", "-o": phyml_optimization, "--model": None, # I will iterate over this value when # creating jobs "--quiet": "" } ModelTesterTask.__init__(self, nodeid, "mchooser", "Prottest", base_args, conf["prottest"]) self.best_model = None self.seqtype = "aa" self.models = self.conf["prottest"]["_models"] self.init() self.post_init()
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, constrain_tree, conf, confname): GLOBALS["citator"].add(PHYML_CITE) self.alg_phylip_file = alg_phylip_file self.alg_fasta_file = alg_fasta_file self.confname = confname self.conf = conf self.lk_mode = conf[confname]["_lk_mode"] if self.lk_mode == "raxml": phyml_optimization = "n" elif self.lk_mode == "phyml": phyml_optimization = "lr" else: raise ValueError("Choose a valid lk_mode value (raxml or phyml)") base_args = { "--datatype": "aa", "--input": self.alg_phylip_file, "--bootstrap": "0", "-o": phyml_optimization, "--model": None, # I will iterate over this value when # creating jobs "--quiet": "" } self.models = conf[confname]["_models"] task_name = "Prottest-[%s]" % ','.join(self.models) ModelTesterTask.__init__(self, nodeid, "mchooser", task_name, base_args, conf[confname]) self.best_model = None self.seqtype = "aa" self.init()