def build_tree(self, infile=None, nodefile=None, root='best'): ''' instantiate a tree object and make a time tree if infiles are None, the tree is build from scratch. Otherwise the tree is loaded from file ''' self.tree = tree(aln=self.seqs.aln, proteins=self.proteins) if infile is None: self.tree.build(root=root) else: self.tree.tt_from_file(infile, nodefile=nodefile, root=root)
def build_tree(self): ''' (1) instantiate a tree object (process.tree) (2) If newick file doesn't exist or isn't valid: build a newick tree (normally RAxML) (3) Make a TimeTree ''' self.tree = tree(aln=self.seqs.aln, proteins=self.proteins, verbose=self.config["subprocess_verbosity_level"]) newick_file = self.output_path + ".newick" if self.try_to_restore and os.path.isfile(newick_file) and self.tree.check_newick(newick_file): self.log.notify("Newick file \"{}\" can be used to restore".format(newick_file)) else: self.log.notify("Building newick tree.") self.tree.build_newick(newick_file, **self.config["newick_tree_options"])
def build_tree(self, infile=None): self.tree = tree(aln=self.seqs.aln, proteins = self.proteins) if infile is None: self.tree.build() else: self.tree.tt_from_file(infile) self.tree.timetree(Tc=0.005, infer_gtr=True, n_iqd=3) for node in self.tree.tt.tree.get_terminals(): if hasattr(node, "bad_branch") and node.bad_branch: node.numdate = min(2016.15, node.numdate) self.tree.add_translations() self.remove_outgroup() self.tree.refine() self.tree.layout()
def build_tree(self): ''' (1) instantiate a tree object (process.tree) (2) If newick file doesn't exist or isn't valid: build a newick tree (normally RAxML) (3) Make a TimeTree ''' # self.log.warn("self.verbose not set") self.tree = tree(aln=self.seqs.aln, proteins=self.proteins, verbose=0) newick_file = self.output_path + ".newick" try: assert (self.try_to_restore == True) assert (os.path.isfile(newick_file)) self.tree.check_newick(newick_file) self.log.notify( "Newick file restored from \"{}\"".format(newick_file)) except AssertionError: self.tree.build_newick(newick_file, **self.config["newick_tree_options"])
def build_tree(self, infile=None, nodefile=None, root='best'): ''' instantiate a tree object and make a time tree if infiles are None, the tree is build from scratch. Otherwise the tree is loaded from file ''' self.tree = tree(aln=self.seqs.aln, proteins = self.proteins) if infile is None: self.tree.build(root=root) else: self.tree.tt_from_file(infile, nodefile=nodefile, root=root) # if node file is none, no time information is available. # hence make a coalescent model time tree and decorate that tree. if nodefile is None: self.tree.timetree(Tc=0.01, infer_gtr=True) self.tree.add_translations() self.tree.refine() self.tree.layout()