def prob_locus_coal_recon_topology_samples(
coal_tree, coal_recon,
locus_tree, locus_recon, locus_events, popsizes,
stree, stimes,
daughters, duprate, lossrate, nsamples,
pretime=None, premean=None):
if dlcoalc:
# sample some reason branch lengths just for logging purposes
locus_times = duploss.sample_dup_times(
locus_tree, stree, locus_recon, duprate, lossrate, pretime,
premean,
events=locus_events)
treelib.set_dists_from_timestamps(locus_tree, locus_times)
# use C code
return coal.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)
else:
# python backup
prob = 0.0
for i in xrange(nsamples):
# sample duplication times
locus_times = duploss.sample_dup_times(
locus_tree, stree, locus_recon, duprate, lossrate, pretime,
premean,
events=locus_events)
treelib.set_dists_from_timestamps(locus_tree, locus_times)
# coal topology probability
coal_prob = prob_locus_coal_recon_topology(
coal_tree, coal_recon, locus_tree, popsizes, daughters)
prob += exp(coal_prob)
prob = util.safelog(prob / nsamples)
return prob
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_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):
"""
Evaluate terms that depend on T^G and R^G.
That is, fix T^L, R^L, and daughters and evaluate the double integral:
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
This is the probability we used in the searching process.
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
"""
locus_events = phylo.label_events(locus_tree, locus_recon)
# optimize the parameters
# util.tic("optimize parameter")
# rates, freqs, alphas = pllprob.optimize_parameters(alnfile, partfile, coal_tree,
# threads=threads, seed=seed, eps=eps)
# util.toc()
# double integral
double_integral_list = []
double_integral = 0.0
util.tic("recon prob")
for i in xrange(nsamples_locus):
# sample t^L, the unit should be in myr
#util.tic("topo prob")
locus_times = duploss.sample_dup_times(locus_tree,
stree,
locus_recon,
duprate,
lossrate,
pretime,
premean,
events=locus_events)
treelib.set_dists_from_timestamps(locus_tree, locus_times)
# calculate P(T^G, R^G | T^L, t^L, daughters, theta)
topology_prob = prob_locus_coal_recon_topology(coal_tree, coal_recon,
locus_tree, popsizes,
daughters)
#util.toc()
# for a fixed t^L, compute coal_prob
# sample t^G for topology and compute the probabililty of observing the alignment using MonteCarlo integration
coal_prob = 0.0
alignment_prob_MonteCarlo = 0.0
alignment_prob_list = []
# check probability of lineage counts for this locus tree
zero_lineage_prob = False
#util.tic("set times")
for lnode in locus_tree:
lineages = coal.count_lineages_per_branch(coal_tree, coal_recon,
locus_tree)
bottom_num, top_num = lineages[lnode]
if lnode.parent:
T = lnode.dist
else:
T = util.INF
popsizes = popsizes
lineage_prob = prob_coal_counts(bottom_num, top_num, T, popsizes)
# set zero_lineage_prob = TRUE if one lineage returns zero probability
if (lineage_prob == 0.0):
zero_lineage_prob = True
#util.toc()
# if lineage_prob is zero, coal_prob is zero
if zero_lineage_prob:
coal_prob = -float("inf")
# otherwise, we calculate the coal_prob
else:
for j in xrange(nsamples_coal):
# sample coal times and set the coal_tree accordingly
# locus tree branch lengths are in myr
# make sure the input popsizes are scaled to fit the time unit (typically myr)
try:
sample_coal_times_topology(coal_tree, coal_recon,
locus_tree, popsizes)
except (ZeroDivisionError, ValueError):
# bad sample
util.log("bad sample")
alignment_prob = -util.INF
continue
#===============================================================================
# (log) probability of observing the alignment
#util.tic("alignment probability")
# convert branch lengths from myr to sub/site
for node in coal_tree:
node.dist *= subrate
#util.tic("alignment prob")
# set a regularization parameter beta
print beta
alignment_prob = beta * prob_alignment(alnfile,
partfile,
coal_tree,
rates,
freqs,
alphas,
threads=threads,
seed=seed,
eps=eps)
#util.toc()
### util.log("p = %.6f" % alignment_prob)
#util.toc()
#===============================================================================
### util.log(" log p = %.6g" % alignment_prob)
### util.log(" p = %.6g" % exp(alignment_prob))
alignment_prob_list.append(alignment_prob)
### util.log("p = %f" % alignment_prob_MonteCarlo)
# log_sum_exp function exponentiate the log probability of observing alignment,
# add them up, and take log again
if len(alignment_prob_list) == 0:
# all bad samples
alignment_prob_MonteCarlo = -util.INF
else:
alignment_prob_MonteCarlo = log_sum_exp(
alignment_prob_list) - log(nsamples_coal)
# P(T^G, R^G | T^L, t^L, daughters, theta) * $ P(t^G | ~) * P(A | T^G,t^G) dtG
# coal_prob is a log probability
coal_prob += topology_prob + alignment_prob_MonteCarlo
# add coal probability to a list for further processing
double_integral_list.append(coal_prob)
# log_sum_exp function exponentiate the log probability of observing alignment,
# add them up, and take log again
double_integral = log_sum_exp(double_integral_list) - log(
nsamples_locus)
# logging info
if info is not None:
info["topology_prob"] = topology_prob # one sample of t^L
info[
"alignment_prob"] = alignment_prob_MonteCarlo # one sample of t^L, averaged over t^G
info["coal_prob"] = double_integral
util.toc()
return double_integral