def dup_loss_topology_prior(tree, stree, recon, birth, death, maxdoom=20, events=None):
"""
Returns the log prior of a gene tree topology according to dup-loss model
"""
def gene2species(gene):
return recon[tree.nodes[gene]].name
if events is None:
events = phylo.label_events(tree, recon)
leaves = set(tree.leaves())
phylo.add_implied_spec_nodes(tree, stree, recon, events)
pstree, snodes, snodelookup = spidir.make_ptree(stree)
# get doomtable
doomtable = calc_doom_table(stree, birth, death, maxdoom)
prod = 0.0
for node in tree:
if events[node] == "spec":
for schild in recon[node].children:
nodes2 = [x for x in node.children if recon[x] == schild]
if len(nodes2) > 0:
node2 = nodes2[0]
subleaves = get_sub_tree(node2, schild, recon, events)
nhist = birthdeath.num_topology_histories(node2, subleaves)
s = len(subleaves)
thist = stats.factorial(s) * stats.factorial(s - 1) / 2 ** (s - 1)
if len(set(subleaves) & leaves) == 0:
# internal
prod += log(num_redundant_topology(node2, gene2species, subleaves, True))
else:
# leaves
prod += log(num_redundant_topology(node2, gene2species, subleaves, False))
else:
nhist = 1.0
thist = 1.0
s = 0
t = sum(
stats.choose(s + i, i)
* birthdeath.prob_birth_death1(s + i, schild.dist, birth, death)
* exp(doomtable[snodelookup[schild]]) ** i
for i in range(maxdoom + 1)
)
prod += log(nhist) - log(thist) + log(t)
# correct for renumbering
nt = num_redundant_topology(tree.root, gene2species)
prod -= log(nt)
# phylo.removeImpliedSpecNodes(tree, recon, events)
treelib.remove_single_children(tree)
return prod
def prob_coal_recon_topology(tree, recon, locus_tree, n, daughters):
"""
Returns the log probability of a reconciled gene tree ('tree', 'recon')
from the coalescent model given a locus_tree 'locus_tree',
population sizes 'n', and daughters set 'daughters'
"""
# init population sizes
popsizes = coal.init_popsizes(locus_tree, n)
# log probability
lnp = 0.0
nodes = set(tree.postorder())
# init reverse reconciliation
rev_recon = {}
for node, snode in recon.iteritems():
if node not in nodes:
raise Exception("node '%s' not in tree" % node.name)
rev_recon.setdefault(snode, []).append(node)
# init lineage counts
lineages = {}
for snode in locus_tree:
if snode.is_leaf():
lineages[snode] = len([x for x in rev_recon[snode]
if x.is_leaf()])
else:
lineages[snode] = 0
# iterate through species tree branches
for snode in locus_tree.postorder():
if snode.parent:
# non root branch
u = lineages[snode]
# subtract number of coals in branch
v = u - len([x for x in rev_recon.get(snode, [])
if not x.is_leaf()])
lineages[snode.parent] += v
if snode not in daughters:
try:
lnp += util.safelog(
coal.prob_coal_counts(u, v, snode.dist,
popsizes[snode.name]))
except:
print u, v, snode.dist, popsizes[snode.name]
raise
else:
assert v == 1
lnp -= util.safelog(coal.num_labeled_histories(u, v))
else:
# normal coalesent
u = lineages[snode]
lnp -= util.safelog(coal.num_labeled_histories(u, 1))
# correct for topologies H(T)
# find connected subtrees that are in the same species branch
subtrees = []
subtree_root = {}
for node in tree.preorder():
if node.parent and recon[node] == recon[node.parent]:
subtree_root[node] = subtree_root[node.parent]
else:
subtrees.append(node)
subtree_root[node] = node
# find leaves through recursion
def walk(node, subtree, leaves):
if node.is_leaf():
leaves.append(node)
elif (subtree_root[node.children[0]] != subtree and
subtree_root[node.children[1]] != subtree):
leaves.append(node)
else:
for child in node.children:
walk(child, subtree, leaves)
# apply correction for each subtree
for subtree in subtrees:
leaves = []
for child in subtree.children:
walk(subtree, subtree, leaves)
if len(leaves) > 2:
lnp += util.safelog(
birthdeath.num_topology_histories(subtree, leaves))
return lnp
def dup_loss_topology_prior(tree,
stree,
recon,
birth,
death,
maxdoom=20,
events=None):
"""
Returns the log prior of a gene tree topology according to dup-loss model
"""
def gene2species(gene):
return recon[tree.nodes[gene]].name
if events is None:
events = phylo.label_events(tree, recon)
leaves = set(tree.leaves())
phylo.add_implied_spec_nodes(tree, stree, recon, events)
pstree, snodes, snodelookup = spidir.make_ptree(stree)
# get doomtable
doomtable = calc_doom_table(stree, birth, death, maxdoom)
prod = 0.0
for node in tree:
if events[node] == "spec":
for schild in recon[node].children:
nodes2 = [x for x in node.children if recon[x] == schild]
if len(nodes2) > 0:
node2 = nodes2[0]
subleaves = get_sub_tree(node2, schild, recon, events)
nhist = birthdeath.num_topology_histories(node2, subleaves)
s = len(subleaves)
thist = stats.factorial(s) * stats.factorial(s - 1) / 2**(
s - 1)
if len(set(subleaves) & leaves) == 0:
# internal
prod += log(
num_redundant_topology(node2, gene2species,
subleaves, True))
else:
# leaves
prod += log(
num_redundant_topology(node2, gene2species,
subleaves, False))
else:
nhist = 1.0
thist = 1.0
s = 0
t = sum(
stats.choose(s + i, i) * birthdeath.prob_birth_death1(
s + i, schild.dist, birth, death) *
exp(doomtable[snodelookup[schild]])**i
for i in range(maxdoom + 1))
prod += log(nhist) - log(thist) + log(t)
# correct for renumbering
nt = num_redundant_topology(tree.root, gene2species)
prod -= log(nt)
#phylo.removeImpliedSpecNodes(tree, recon, events)
treelib.remove_single_children(tree)
return prod