def eval_proposal(self, proposal):
"""Compute probability of proposal"""
#util.tic("eval")
# compute recon probability
info = {}
# DEBUG
counts = coal.count_lineages_per_branch(self.coal_tree,
proposal.coal_recon,
proposal.locus_tree)
maxcount = max(x[0] for x in counts.values())
#util.logger("max lineage count %d" % maxcount)
if maxcount > 10:
return -util.INF
p = dlcoal.prob_dlcoal_recon_topology(self.coal_tree,
proposal.coal_recon,
proposal.locus_tree,
proposal.locus_recon,
proposal.locus_events,
proposal.daughters,
self.stree, self.n,
self.duprate, self.lossrate,
self.pretime, self.premean,
nsamples=self.nsamples,
add_spec=False,
info=info)
proposal.data = info
#util.toc()
return p
for node in fly_stree:
node.dist *= gen_per_myr # (convert to generations)
n = int(100e6) * 2
duprate = .0012 / gen_per_myr
lossrate = .0011 / gen_per_myr
coal_tree, ex = dlcoal.sample_dlcoal(fly_stree, n, duprate, lossrate)
#draw_tree_names(coal_tree, scale=1e-7)
if 0:
draw_tree_names(coal_tree, scale=.5e-7)
print exp(dlcoal.prob_dlcoal_recon_topology(
coal_tree, ex["coal_recon"],
ex["locus_tree"], ex["locus_recon"], ex["locus_events"],
ex["daughters"], fly_stree, n, duprate, lossrate,
pretime=None, premean=None,
maxdoom=20, nsamples=100,
add_spec=True))
if 0:
draw_tree_names(coal_tree, scale=.5e-7, minlen=8)
draw_tree_names(ex["locus_tree"], scale=.5e-7, minlen=8)
print exp(dlcoal.prob_multicoal_recon_topology(
coal_tree, ex["coal_recon"], ex["locus_tree"], n, ex["daughters"]))
print exp(dlcoal.prob_multicoal_recon_topology2(
coal_tree, ex["coal_recon"], ex["locus_tree"], n, ex["daughters"]))
if 0:
draw_tree_names(coal_tree, scale=1e-7)
def eval_proposal(self, proposal):
"""Compute probability of proposal"""
### util.tic("eval")
# proposal.coal_tree.write()
# compute recon probability
info = {}
# DEBUG
counts = coal.count_lineages_per_branch(proposal.coal_tree,
proposal.coal_recon,
proposal.locus_tree)
maxcount = max(x[0] for x in counts.values())
# util.logger("max lineage count %d" % maxcount)
# do not continue if there are too many deep coalescences
if maxcount > 10:
return -util.INF
# estimate coal_tree
if self.stage == "coal_tree":
#util.tic("reconprob")
p = reconprob.prob_gene_species_alignment_recon(
self.alnfile,
self.partfile,
self.stree,
self.popsizes,
self.duprate,
self.lossrate,
self.subrate,
self.beta,
self.pretime,
self.premean,
proposal.coal_tree,
proposal.coal_recon,
self.nsamples_coal,
proposal.locus_tree,
proposal.locus_recon,
self.nsamples_locus,
proposal.daughters,
self.rates,
self.freqs,
self.alphas,
self.threads,
self.seed,
self.eps,
info=info)
#util.toc()
"""
p_joint = reconprob.prob_locus_gene_species_alignment_recon(self.alnfile, self.partfile, self.stree,
self.popsizes, self.duprate, self.lossrate, self.subrate, self.beta,
self.pretime, self.premean,
proposal.coal_tree, proposal.coal_recon, self.nsamples_coal,
proposal.locus_tree, proposal.locus_recon, self.nsamples_locus,
proposal.daughters,
self.rates, self.freqs, self.alphas,
self.threads, self.seed, self.eps,
info=info)
util.log("p = %f p_joint = %f [maxp = %f]" % (p, p_joint, self.maxp))
print '(p,p_joint,maxp', (p, p_joint, self.maxp)
"""
# estimate locus_tree
else:
p = dlcoal.prob_dlcoal_recon_topology(
stree=self.stree,
n=self.popsizes,
duprate=self.duprate,
lossrate=self.lossrate,
pretime=self.pretime,
premean=self.premean,
coal_tree=proposal.coal_tree,
coal_recon=proposal.coal_recon,
locus_tree=proposal.locus_tree,
locus_recon=proposal.locus_recon,
locus_events=proposal.locus_events,
daughters=proposal.daughters,
nsamples=self.nsamples_locus,
add_spec=False,
info=info)
"""
p_joint = reconprob.prob_locus_gene_species_alignment_recon(self.alnfile, self.partfile, self.stree,
self.popsizes, self.duprate, self.lossrate, self.subrate, self.beta,
self.pretime, self.premean,
proposal.coal_tree, proposal.coal_recon, self.nsamples_coal,
proposal.locus_tree, proposal.locus_recon, self.nsamples_locus,
proposal.daughters,
self.rates, self.freqs, self.alphas,
self.threads, self.seed, self.eps,
info=info)
util.log("p = %f p_joint = %f [maxp = %f]" % (p, p_joint, self.maxp))
print '(p,p_joint,maxp', (p, p_joint, self.maxp)
"""
proposal.data = info
#util.toc()
return p