def compute_cost(self, gtree):
"""Returns the duplication-loss cost"""
recon = phylo.reconcile(gtree, self.stree, self.gene2species)
events = phylo.label_events(gtree, recon)
cost = 0
if self.dupcost != 0:
cost += phylo.count_dup(gtree, events) * self.dupcost
if self.losscost != 0:
cost += phylo.count_loss(gtree, self.stree, recon) * self.losscost
return cost
def eval_proposal(self, proposal):
"""Compute cost of proposal"""
if not phyloDLC.assert_daughters(proposal.locus_events, proposal.daughters):
# ensure locus events (duplications) and daughters match
ndup, nloss, ncoal = None, None, None
dupcost, losscost, coalcost = util.INF, util.INF, util.INF
else:
# find dup cost
if self.dupcost == 0:
ndup = None
dupcost = 0
else:
ndup = phylo.count_dup(proposal.locus_tree, proposal.locus_events)
dupcost = ndup * self.dupcost
# find loss cost
if self.losscost == 0:
nloss = None
losscost = 0
else:
nloss = phylo.count_loss(proposal.locus_tree, self.stree, proposal.locus_recon)
losscost = nloss * self.losscost
# find coal cost (first ensure bounded coalescent is satisfied - should always be true based on how daughters are proposed)
phyloDLC.assert_bounded_coal(self.coal_tree, proposal.coal_recon, proposal.locus_tree, proposal.daughters)
if self.coalcost == 0:
ncoal = None
coalcost = 0
else:
# add implied speciation nodes if desired
# this must be added AFTER counting dups and losses since it affects loss inference
if self.implied:
added = phylo.add_implied_spec_nodes(proposal.locus_tree, self.stree,
proposal.locus_recon, proposal.locus_events)
ncoal = phyloDLC.count_coal(self.coal_tree, proposal.coal_recon, proposal.locus_tree)
coalcost = ncoal * self.coalcost
if self.implied:
phylo.remove_implied_spec_nodes(proposal.locus_tree, added,
proposal.locus_recon, proposal.locus_events)
# total cost
cost = dupcost + losscost + coalcost
# logging info
info = {}
info["ndup"] = ndup
info["nloss"] = nloss
info["ncoal"] = ncoal
info["cost"] = cost
proposal.data = info
return cost
def _compute_duplosscost(self, ltree):
"""Returns dup/loss cost from locus tree to species tree"""
cost = 0
if self.dupcost > 0 or self.losscost > 0:
recon = phylo.reconcile(ltree, self.stree, self.gene2species)
events = phylo.label_events(ltree, recon)
if self.dupcost != 0:
cost += phylo.count_dup(ltree, events) * self.dupcost
if self.losscost != 0:
cost += phylo.count_loss(ltree, self.stree, recon) * self.losscost
return cost
def _compute_coalcost(self, gtree, ltree):
"""Returns deep coalescent cost from coalescent tree (gene tree) to locus tree
Note: uses Zhang (RECOMB 2000) result that C = L - 2*D
"""
cost = 0
if self.coalcost > 0:
recon = phylo.reconcile(gtree, ltree)
events = phylo.label_events(gtree, recon)
cost = (phylo.count_loss(gtree, ltree, recon) - 2*phylo.count_dup(gtree, events)) * self.coalcost
return cost
def prescreen(self, tree):
recon = phylo.reconcile(tree, self.stree, self.gene2species)
events = phylo.label_events(tree, recon)
if self.dupcost == 0:
dupcost = 0
else:
ndup = phylo.count_dup(tree, events)
dupcost = ndup * self.dupcost
if self.losscost == 0:
losscost = 0
else:
nloss = phylo.count_loss(tree, self.stree, recon)
losscost = nloss * self.losscost
return dupcost + losscost
def prescreen(self, tree):
recon = phylo.reconcile(tree, self.stree, self.gene2species)
events = phylo.label_events(tree, recon)
if self.dupcost == 0:
dupcost = 0
else:
ndup = phylo.count_dup(tree, events)
dupcost = ndup * self.dupcost
if self.losscost == 0:
losscost = 0
else:
nloss = phylo.count_loss(tree, self.stree, recon)
losscost = nloss * self.losscost
return dupcost + losscost
def eval_proposal(self, proposal):
"""Compute cost of proposal"""
if not phyloDLC.assert_daughters(proposal.locus_events,
proposal.daughters):
# ensure locus events (duplications) and daughters match
ndup, nloss, ncoal = None, None, None
dupcost, losscost, coalcost = util.INF, util.INF, util.INF
else:
# find dup cost
if self.dupcost == 0:
ndup = None
dupcost = 0
else:
ndup = phylo.count_dup(proposal.locus_tree,
proposal.locus_events)
dupcost = ndup * self.dupcost
# find loss cost
if self.losscost == 0:
nloss = None
losscost = 0
else:
nloss = phylo.count_loss(proposal.locus_tree, self.stree,
proposal.locus_recon)
losscost = nloss * self.losscost
# find coal cost (first ensure bounded coalescent is satisfied - should always be true based on how daughters are proposed)
phyloDLC.assert_bounded_coal(self.coal_tree, proposal.coal_recon,
proposal.locus_tree,
proposal.daughters)
if self.coalcost == 0:
ncoal = None
coalcost = 0
else:
# add implied speciation nodes if desired
# this must be added AFTER counting dups and losses since it affects loss inference
if self.implied:
added = phylo.add_implied_spec_nodes(
proposal.locus_tree, self.stree, proposal.locus_recon,
proposal.locus_events)
ncoal = phyloDLC.count_coal(self.coal_tree,
proposal.coal_recon,
proposal.locus_tree)
coalcost = ncoal * self.coalcost
if self.implied:
phylo.remove_implied_spec_nodes(proposal.locus_tree, added,
proposal.locus_recon,
proposal.locus_events)
# total cost
cost = dupcost + losscost + coalcost
# logging info
info = {}
info["ndup"] = ndup
info["nloss"] = nloss
info["ncoal"] = ncoal
info["cost"] = cost
proposal.data = info
return cost
def prob_dlcoal_recon_topology(coal_tree, coal_recon,
locus_tree, locus_recon, locus_events,
daughters,
stree, n, duprate, lossrate,
pretime=None, premean=None,
maxdoom=20, nsamples=100,
add_spec=True):
"""
Probability of a reconcile gene tree in the DLCoal model.
coal_tree -- coalescent tree
coal_recon -- reconciliation of coalescent tree to locus tree
locus_tree -- locus tree (has dup-loss)
locus_recon -- reconciliation of locus tree to species tree
locus_events -- events dict for locus tree
stree -- species tree
n -- population sizes in species tree
duprate -- duplication rate
lossrate -- loss rate
You must also specify one of the following
pretime -- starting time before species tree
premean -- mean starting time before species tree
Note: locus tree must have implied speciation nodes present
"""
dups = phylo.count_dup(locus_tree, locus_events)
# ensure implicit speciations are present
if add_spec:
phylo.add_implied_spec_nodes(locus_tree, stree,
locus_recon, locus_events)
# init popsizes for locus tree
stree_popsizes = coal.init_popsizes(stree, n)
popsizes = {}
for node in locus_tree:
popsizes[node.name] = stree_popsizes[locus_recon[node].name]
# duploss probability
util.tic("top")
dl_prob = spidir.calc_birth_death_prior(locus_tree, stree, locus_recon,
duprate, lossrate,
maxdoom=maxdoom)
util.toc()
# daughters probability
d_prob = dups * log(.5)
# integrate over duplication times using sampling
prob = 0.0
#util.tic("int")
for i in xrange(nsamples):
# sample duplication times
locus_times = spidir.topology_prior.sample_dup_times(
locus_tree, stree, locus_recon, duprate, lossrate, pretime,
premean,
events=locus_events)
assert len(locus_times) == len(locus_tree.nodes), (
len(locus_times), len(locus_tree.nodes))
treelib.set_dists_from_timestamps(locus_tree, locus_times)
# coal topology probability
coal_prob = prob_coal_recon_topology(coal_tree, coal_recon,
locus_tree, popsizes, daughters)
prob += exp(coal_prob)
print coal_prob
#util.toc()
return dl_prob + d_prob + util.safelog(prob / nsamples)
def prob_dlcoal_recon_topology(coal_tree, coal_recon,
locus_tree, locus_recon, locus_events,
daughters,
stree, n, duprate, lossrate,
pretime=None, premean=None,
nsamples=100,
add_spec=True, info=None):
"""
Probability of a reconcile gene tree in the DLCoal model.
coal_tree -- coalescent tree
coal_recon -- reconciliation of coalescent tree to locus tree
locus_tree -- locus tree (has dup-loss)
locus_recon -- reconciliation of locus tree to species tree
locus_events -- events dict for locus tree
stree -- species tree
n -- population sizes in species tree
duprate -- duplication rate
lossrate -- loss rate
You must also specify one of the following
pretime -- starting time before species tree
premean -- mean starting time before species tree
"""
# init popsizes for locus tree
stree_popsizes = coal.init_popsizes(stree, n)
popsizes = {}
for node in locus_tree:
popsizes[node.name] = stree_popsizes[locus_recon[node].name]
# duploss probability
dl_prob = duploss.prob_dup_loss(
locus_tree, stree, locus_recon, locus_events,
duprate, lossrate)
# daughters probability
dups = phylo.count_dup(locus_tree, locus_events)
d_prob = dups * log(.5)
# integrate over duplication times using sampling
stimes = treelib.get_tree_timestamps(stree)
prob = prob_locus_coal_recon_topology_samples(
coal_tree, coal_recon,
locus_tree, locus_recon, locus_events, popsizes,
stree, stimes,
daughters, duprate, lossrate, nsamples,
pretime, premean)
# logging info
if info is not None:
info["duploss_prob"] = dl_prob
info["daughters_prob"] = d_prob
info["coal_prob"] = prob
info["prob"] = dl_prob + d_prob + prob - log(nsamples)
return dl_prob + d_prob + prob - log(nsamples)
def prob_locus_gene_species_alignment_recon(alnfile,
partfile,
stree,
popsizes,
duprate,
lossrate,
subrate,
beta,
pretime,
premean,
coal_tree,
coal_recon,
nsamples_coal,
locus_tree,
locus_recon,
nsamples_locus,
daughters,
rates,
freqs,
alphas,
threads=1,
seed=ALIGNMENT_SEED,
eps=0.1,
info=None):
"""
(Log) probability of the joint probability of locus_tree, locus_recon, coal_tree,
coal_recon, daughters and alignment. Mathematically, it computes:
P(T^G, T^L, R^G, R^L, delta^L, A | S, theta) = P(delta^L | T^L, R^L, S) + P(T^L, R^L | S, theta^S) +
int int P(t^L | T^L, R^L, S, theta) * P(T^G, R^G, t^G | t^L, T^L, daughters, R^L, theta) * P(A | T^G, t^G) dt^L dt^G
alnfile -- alignment file
partfile -- partition file
stree -- species tree
popsizes -- population sizes in species tree
duprate -- duplication rate
lossrate -- loss rate
subrate -- substitution rate
beta -- regularization parameter
pretime -- starting time before species tree
premean -- mean starting time before species tree
coal_tree -- coalescent tree
coal_recon -- reconciliation of coalescent tree to locus tree
nsamples_coal -- number of times to sample coal times t^G
locus_tree -- locus tree (has dup-loss)
locus_recon -- reconciliation of locus tree to species tree
nsamples_locus -- number of times to sample the locus tree times t^L
daughters -- daughter nodes
rates, freqs, alphas -- optimization parameters
Note: Adapted from dlcoal.prob_dlcoal_recon_topology(...) [in __init.py]
"""
# duploss proability: P(T^L, R^L | S, theta)
locus_events = phylo.label_events(locus_tree, locus_recon)
dl_prob = duploss.prob_dup_loss(locus_tree, stree, locus_recon,
locus_events, duprate, lossrate)
# daughters probability: P(daughters | T^L, R^L, S)
dups = phylo.count_dup(locus_tree, locus_events)
daughter_prob = dups * log(.5)
# double integral
double_integral = prob_gene_species_alignment_recon(alnfile,
partfile,
stree,
popsizes,
duprate,
lossrate,
subrate,
beta,
pretime,
premean,
coal_tree,
coal_recon,
nsamples_coal,
locus_tree,
locus_recon,
nsamples_locus,
daughters,
rates,
freqs,
alphas,
threads=1,
seed=ALIGNMENT_SEED,
eps=0.1,
info=None)
return dl_prob + daughter_prob + double_integral