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()