def _label(tree, ancestors):
"""
Relabel internal nodes of a tree and map them to the corresponding name of
ancestral sequences.
:param tree: str, a NEWICK format string or file for a tree (must start with
"(" and end with ';').
:param ancestors: dict, a dict object stores sequences.
:return: tuple, a relabeled tree object and a dict object for sequences.
"""
if isinstance(tree, str):
if os.path.isfile(tree):
pass
elif tree.startswith('(') and tree.endswith(';'):
tree = StringIO(tree)
else:
error('Invalid tree encounter, tree relabel aborted.')
sys.exit(1)
tree = Phylo.read(tree, 'newick')
number, maps = tree.count_terminals(), {}
for clade in tree.find_clades():
if not clade.is_terminal():
clade.confidence = None
number += 1
old, new = clade.name, 'NODE{}'.format(number)
maps[old] = new
clade.name = new
ancestors = {maps.get(k, k): v for k, v in ancestors.items()}
return tree, ancestors
