def recon_root(self, gtree, newCopy=True, returnCost=False):
"""
Reroots the tree by minimizing the cost function.
Rerooted tree must keep same node names as the original tree.
Adapted from phylo.recon_root.
"""
# try all rerootings
mincost = util.INF
for gtree, edge in self._reroot_helper(gtree,
newCopy=newCopy,
returnEdge=True):
cost = self.compute_cost(gtree)
if cost < mincost:
mincost = cost
minroot = edge
# root tree by minroot
if edge != minroot:
node1, node2 = minroot
if node1.parent != node2:
node1, node2 = node2, node1
assert node1.parent == node2
treelib.reroot(gtree, node1.name, newCopy=False, keepName=True)
if returnCost:
return gtree, mincost
else:
return gtree
def unroot(gtree, newCopy=True):
"""returns unrooted gtree (with internal root always at the same place)"""
if newCopy:
gtree = gtree.copy()
treelib.unroot(gtree, newCopy=False)
treelib.reroot(gtree,
gtree.nodes[sorted(gtree.leaf_names())[0]].parent.name,
onBranch=False,
newCopy=False)
return gtree
def _reroot_helper(self, gtree, newCopy=True, returnEdge=False):
"""
Yields rerooted trees.
Adapted from phylo.recon_root.
"""
# make a consistent unrooted copy of gene tree
if newCopy:
gtree = gtree.copy()
if len(gtree.leaves()) == 2:
raise StopIteration
oldroot = gtree.root.name
treelib.unroot(gtree, newCopy=False)
treelib.reroot(gtree,
gtree.nodes[sorted(gtree.leaf_names())[0]].parent.name,
onBranch=False,
newCopy=False)
# make rerooting order consistent using hash ordering
phylo.hash_order_tree(gtree, self.gene2species)
# get list of edges to root on
edges = []
def walk(node):
edges.append((node, node.parent))
if not node.is_leaf():
node.recurse(walk)
edges.append((node, node.parent))
for child in gtree.root.children:
walk(child)
# try initial root
treelib.reroot(gtree, edges[0][0].name, newCopy=False)
gtree.rename(gtree.root.name, oldroot)
if returnEdge:
yield gtree, edges[0]
else:
yield gtree
rootedge = sorted(edges[0])
# try rerooting on everything
for edge in edges[1:]:
if sorted(edge) == rootedge:
continue
rootedge = sorted(edge)
node1, node2 = edge
if node1.parent != node2:
node1, node2 = node2, node1
assert node1.parent == node2, "%s %s" % (node1.name, node2.name)
# new root and cost
treelib.reroot(gtree, node1.name, newCopy=False, keepName=True)
if returnEdge:
yield gtree, edge
else:
yield gtree