def sample_dlcoal_no_ifix(stree, n, freq, duprate, lossrate, freqdup, freqloss,\
forcetime, namefunc=lambda x: x, \
remove_single=True, name_internal="n", minsize=0):
"""Sample a gene tree from the DLCoal model using the new simulator"""
# generate the locus tree
while True:
locus_tree, locus_extras = sim_DLILS_gene_tree(stree, n, freq, \
duprate, lossrate, \
freqdup, freqloss, \
forcetime)
if len(locus_tree.leaves()) >= minsize:
break
if len(locus_tree.nodes) <= 1: # TODO: check 1 value
# total extinction
coal_tree = treelib.Tree()
coal_tree.make_root()
coal_recon = {coal_tree.root: locus_tree.root}
daughters = set()
else:
# simulate coalescence
# create new (expanded) locus tree
logged_locus_tree, logged_extras = locus_to_logged_tree(locus_tree, popsize = n)
daughters = logged_extras[0]
pops = logged_extras[1]
log_recon = logged_extras[2]
# treelib.assert_tree(logged_locus_tree)
# removed locus_tree_copy from below
coal_tree, coal_recon = dlcoal.sample_locus_coal_tree(logged_locus_tree,
n=pops, daughters=daughters,
namefunc=lambda lognamex: log_recon[lognamex] + '_' + str(lognamex))
# print set(coal_tree) - set(coal_tree.postorder())
treelib.assert_tree(coal_tree)
# clean up coal tree
if remove_single:
treelib.remove_single_children(coal_tree)
phylo.subset_recon(coal_tree, coal_recon)
if name_internal:
dlcoal.rename_nodes(coal_tree, name_internal)
dlcoal.rename_nodes(locus_tree, name_internal)
# store extra information
### TODO: update this now that we're using logged locus tree, new sample function
extra = {"locus_tree": locus_tree,
"locus_recon": locus_extras['recon'],
"locus_events": locus_extras['events'],
"coal_tree": coal_tree,
"coal_recon": coal_recon,
"daughters": daughters}
return coal_tree, extra
def recon_helper(self, nsearch=1000):
"""Perform reconciliation"""
self.maxp = -util.INF
self.maxrecon = None
proposal = self.proposer.init_proposal()
init_proposal = proposal.copy()
for i in xrange(nsearch):
if i % 10 == 0:
print "search", i
# evaluate the probability of proposal
util.tic("eval")
p = self.eval_proposal(proposal)
util.toc()
# evaluate the search, then keep or discard the proposal
util.tic("prop")
self.eval_search(p, proposal)
proposal = self.proposer.next_proposal() # set the next proposal
util.toc()
# all proposals bad, use initial proposal
if not self.maxrecon:
self.maxrecon = init_proposal
# rename locus tree nodes
dlcoal.rename_nodes(self.maxrecon.locus_tree,
self.name_internal) # how about coal_tree names?
return self.maxrecon
def next_proposal(self):
# if leaves <= 2, no need to propose another tree
if len(self._coal_search.get_tree().leaves()) <= 2:
return self._recon
# always tree now because _num_coal_recon is set 0
if self._i_coal_recons >= self._num_coal_recons:
# propose new locus_tree
# if locus_tree has not yet been accepted, then revert it
if not self._accept_coal:
self._coal_search.revert()
# propose a new coal tree using _coal_search
self._coal_search.propose()
self._accept_coal = False
self._i_coal_recons = 1
# set coal_tree to be the proposed one
coal_tree = self._coal_search.get_tree().copy()
# make recon root optimal
phylo.recon_root(coal_tree, self._locus_tree, newCopy=False)
dlcoal.rename_nodes(coal_tree)
# propose remaining parts of dlcoal recon
# reconciliation is given by lca
self._recon = self._recon_lca(coal_tree)
else:
# modify coal_recon
try:
self._i_coal_recons += 1
self._coal_recon_enum.next()
except StopIteration:
self._i_coal_recon = self._num_coal_recons
return self.next_proposal()
return self._recon
def recon(self, nsearch=1000):
"""Perform reconciliation"""
self.init_search()
proposal = self.proposer.init_proposal()
self.maxrecon = proposal.copy()
for i in xrange(nsearch):
if i % 10 == 0:
print "search", i
util.tic("eval")
p = self.eval_proposal(proposal)
util.toc()
util.tic("prop")
self.eval_search(p, proposal)
proposal = self.proposer.next_proposal()
util.toc()
# rename locus tree nodes
dlcoal.rename_nodes(self.maxrecon.locus_tree, self.name_internal)
return self.maxrecon
def next_proposal(self):
if len(self._locus_search.get_tree().leaves()) <= 2:
return self._recon
if self._i_coal_recons >= self._num_coal_recons:
# propose new locus_tree
# if locus_tree has not yet been accepted, then revert it
if not self._accept_locus:
self._locus_search.revert()
self._locus_search.propose()
self._accept_locus = False
self._i_coal_recons = 0
locus_tree = self._locus_search.get_tree().copy()
# TODO: make recon root optional
phylo.recon_root(locus_tree, self._stree,
self._gene2species,
newCopy=False)
dlcoal.rename_nodes(locus_tree)
# propose remaining parts of dlcoal recon
self._recon = self._recon_lca(locus_tree)
else:
# modify coal_recon
try:
self._i_coal_recons += 1
self._coal_recon_enum.next()
except StopIteration:
self._i_coal_recon = self._num_coal_recons
return self.next_proposal()
return self._recon
def sample_dlcoal(stree, n, duprate, lossrate,
leaf_counts=None,
namefunc=lambda x: x,
remove_single=True, name_internal="n",
minsize=0, reject=False):
"""Sample a gene tree from the DLCoal model"""
# generate the locus tree
while True:
# TODO: does this take a namefunc?
locus_tree, locus_recon, locus_events = \
birthdeath.sample_birth_death_gene_tree(
stree, duprate, lossrate)
if len(locus_tree.leaves()) >= minsize:
break
# if n is a dict, update it with gene names from locus tree
if isinstance(n, dict):
n2 = {}
for node, snode in locus_recon.iteritems():
n2[node.name] = n[snode.name]
else:
n2 = n
# if leaf_counts is a dict, update it with gene names from locus tree
# TODO: how to handle copy number polymorphism?
if isinstance(leaf_counts, dict):
leaf_counts2 = {}
for node in locus_tree.leaves():
snode = locus_recon[node]
leaf_counts2[node.name] = leaf_counts[snode.name]
else:
leaf_counts2 = leaf_counts
if len(locus_tree.nodes) <= 1:
# total extinction
coal_tree = treelib.Tree()
coal_tree.make_root()
coal_recon = {coal_tree.root: locus_tree.root}
daughters = set()
else:
# simulate coalescence
# choose daughter duplications
daughters = set()
for node in locus_tree:
if locus_events[node] == "dup":
daughters.add(node.children[random.randint(0, 1)])
if reject:
# use slow rejection sampling (for testing)
coal_tree, coal_recon = sample_multilocus_tree_reject(
locus_tree, n2, leaf_counts=leaf_counts2, daughters=daughters, namefunc=namefunc)
else:
coal_tree, coal_recon = sample_multilocus_tree(
locus_tree, n2, leaf_counts=leaf_counts2, daughters=daughters, namefunc=namefunc)
# clean up coal tree
if remove_single:
treelib.remove_single_children(coal_tree)
phylo.subset_recon(coal_tree, coal_recon)
if name_internal:
dlcoal.rename_nodes(coal_tree, name_internal)
dlcoal.rename_nodes(locus_tree, name_internal)
# store extra information
extra = {"locus_tree": locus_tree,
"locus_recon": locus_recon,
"locus_events": locus_events,
"coal_tree": coal_tree,
"coal_recon": coal_recon,
"daughters": daughters}
return coal_tree, extra
def sample_dlcoal_hem(stree, n, duprate, lossrate,
freq, freqdup, freqloss, steptime,
namefunc=lambda x: x,
keep_extinct=False,
remove_single=True,
name_internal="n", minsize=0):
"""Sample a gene tree from the DLCoal model with hemiplasy"""
# generate the locus tree
while True:
locus_tree, locus_extras = sample_locus_tree_hem(
stree, n, duprate, lossrate,
freq, freqdup, freqloss, steptime,
keep_extinct=keep_extinct)
if len(locus_tree.leaves()) >= minsize:
break
if len(locus_tree.nodes) <= 1: # TODO: check 1 value
# total extinction
coal_tree = treelib.Tree()
coal_tree.make_root()
coal_recon = {coal_tree.root: locus_tree.root}
daughters = set()
else:
# simulate coalescence
# create new (expanded) locus tree
logged_locus_tree, logged_extras = locus_to_logged_tree(
locus_tree, popsize=n)
daughters = logged_extras[0]
pops = logged_extras[1]
log_recon = logged_extras[2]
#treelib.assert_tree(logged_locus_tree)
# removed locus_tree_copy from below
coal_tree, coal_recon = dlcoal.sim.sample_multilocus_tree(
logged_locus_tree, n=pops, daughters=daughters,
namefunc=lambda lognamex: log_recon[lognamex]+'_'+str(lognamex))
#print set(coal_tree) - set(coal_tree.postorder())
treelib.assert_tree(coal_tree)
# clean up coal tree
if remove_single:
treelib.remove_single_children(coal_tree)
phylo.subset_recon(coal_tree, coal_recon)
if name_internal:
dlcoal.rename_nodes(coal_tree, name_internal)
dlcoal.rename_nodes(locus_tree, name_internal)
# store extra information
extra = {"locus_tree": locus_tree,
"locus_recon": locus_extras['recon'],
"locus_events": locus_extras['events'],
"coal_tree": coal_tree,
"coal_recon": coal_recon,
"daughters": daughters}
if keep_extinct:
extra["full_locus_tree"] = locus_extras["full_locus_tree"]
return coal_tree, extra