def test_dlcoal_tree(locus_tree, n, daughters, nsamples):
"""test multicoal_tree"""
tops = {}
for i in xrange(nsamples):
if i % (nsamples // 100) == 0:
print i
coal_tree, coal_recon = dlcoal.sample_locus_coal_tree(
locus_tree, n, leaf_counts=None,
daughters=daughters,
namefunc=lambda x: x)
top = phylo.hash_tree(coal_tree)
tops.setdefault(top, [0, coal_tree, coal_recon])[0] += 1
tab = Table(headers=["top", "simple_top", "percent", "prob"])
for top, (num, tree, recon) in tops.items():
tree2 = tree.copy()
treelib.remove_single_children(tree2)
tab.add(top=top,
simple_top=phylo.hash_tree(tree2),
percent=num/float(nsamples),
prob=exp(dlcoal.prob_locus_coal_recon_topology(
tree, recon, locus_tree, n, daughters)))
tab.sort(col="prob", reverse=True)
return tab, tops
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 debug_test3():
stree = treelib.read_tree('examples/nbin.stree') # run from ../ of this directory
for node in stree:
node.dist *= 1e7 # gen per myr
popsize = 2e7
freq = 1e0
dr = .0000012 / 1e7 #.0012/1e7
lr = .0000011 / 1e7 #.0006/1e7
freqdup = freqloss = .05
forcetime = 1e7
for node in stree:
print node.name, node.dist, len(node.children)
print
locus_tree, locus_extras = sim_DLILS_gene_tree(stree, popsize, freq, \
dr, lr, \
freqdup, freqloss, \
forcetime)
for node in locus_tree:
print node.name, node.dist, len(node.children)
print
logged_locus_tree, logged_extras = locus_to_logged_tree(locus_tree, popsize)
daughters = logged_extras[0]
pops = logged_extras[1]
coal_tree, coal_recon = dlcoal.sample_locus_coal_tree(logged_locus_tree,
n=pops, daughters=daughters,
namefunc=lambda x: logged_extras[2][x] + '_' + str(x))
#begin debug
print coal_tree.leaf_names()
try:
# print set(coal_tree) - set(coal_tree.postorder())
treelib.assert_tree(coal_tree)
except AssertionError:
print 'assertion error thrown on coal_tree being a proper tree'
from rasmus import util
hd= util.hist_dict(x.name for x in coal_tree.postorder())
for key in hd.keys():
print key if hd[key]>1 else '',
print
print len(coal_tree.nodes) - len(list(coal_tree.postorder()))
