def sample_birth_death_gene_tree(stree,
birth,
death,
genename=lambda sp, x: sp + "_" + str(x),
removeloss=True):
"""Simulate a gene tree within a species tree with birth and death rates"""
# initialize gene tree
tree = treelib.Tree()
tree.make_root()
recon = {tree.root: stree.root}
events = {tree.root: "spec"}
losses = set()
def walk(snode, node):
if snode.is_leaf():
tree.rename(node.name, genename(snode.name, node.name))
events[node] = "gene"
else:
for child in snode:
# determine if loss will occur
tree2, doom = sample_birth_death_tree(child.dist,
birth,
death,
tree=tree,
node=node,
keepdoom=True)
# record reconciliation
next_nodes = []
def walk2(node):
node.recurse(walk2)
recon[node] = child
if node in doom:
losses.add(node)
events[node] = "gene"
elif node.is_leaf():
events[node] = "spec"
next_nodes.append(node)
else:
events[node] = "dup"
walk2(node.children[-1])
# recurse
for leaf in next_nodes:
walk(child, leaf)
# if no child for node then it is a loss
if node.is_leaf():
losses.add(node)
walk(stree.root, tree.root)
# remove lost nodes
if removeloss:
treelib.remove_exposed_internal_nodes(tree,
set(tree.leaves()) - losses)
treelib.remove_single_children(tree, simplify_root=False)
delnodes = set()
for node in recon:
if node.name not in tree.nodes:
delnodes.add(node)
for node in delnodes:
del recon[node]
del events[node]
if len(tree.nodes) <= 1:
tree.nodes = {tree.root.name: tree.root}
recon = {tree.root: stree.root}
events = {tree.root: "spec"}
return tree, recon, events
def sample_birth_death_gene_tree(stree, birth, death,
genename=lambda sp, x: sp + "_" + str(x),
removeloss=True):
"""Simulate a gene tree within a species tree with birth and death rates"""
# initialize gene tree
tree = treelib.Tree()
tree.make_root()
recon = {tree.root: stree.root}
events = {tree.root: "spec"}
losses = set()
def walk(snode, node):
if snode.is_leaf():
tree.rename(node.name, genename(snode.name, node.name))
events[node] = "gene"
else:
for child in snode:
# determine if loss will occur
tree2, doom = sample_birth_death_tree(
child.dist, birth, death,
tree=tree, node=node, keepdoom=True)
# record reconciliation
next_nodes = []
def walk2(node):
node.recurse(walk2)
recon[node] = child
if node in doom:
losses.add(node)
events[node] = "gene"
elif node.is_leaf():
events[node] = "spec"
next_nodes.append(node)
else:
events[node] = "dup"
walk2(node.children[-1])
# recurse
for leaf in next_nodes:
walk(child, leaf)
# if no child for node then it is a loss
if node.is_leaf():
losses.add(node)
walk(stree.root, tree.root)
# remove lost nodes
if removeloss:
treelib.remove_exposed_internal_nodes(tree,
set(tree.leaves()) - losses)
treelib.remove_single_children(tree, simplify_root=False)
delnodes = set()
for node in recon:
if node.name not in tree.nodes:
delnodes.add(node)
for node in delnodes:
del recon[node]
del events[node]
if len(tree.nodes) <= 1:
tree.nodes = {tree.root.name : tree.root}
recon = {tree.root: stree.root}
events = {tree.root: "spec"}
return tree, recon, events