def test_birth_death_single2_sim(self):
"""test the single branch prior"""
duprate = 2.0
lossrate = .5
T = 1.0
stree = treelib.parse_newick("(A:1,B:1);")
def gene2species(gene):
return gene[:1].upper()
s = stree.leaves()[0]
b = birthDeathCount(1, T, duprate, lossrate)
# 1
tree = treelib.parse_newick("(a,b);")
recon = phylo.reconcile(tree, stree, gene2species)
p = birthDeathCount(1, T, duprate, lossrate) * b
p2 = exp(calcBirthDeathPrior(tree, stree, recon, duprate, lossrate))
p2 *= numRedunantTopology(tree.root, gene2species)
print p, p2
fequal(p, p2)
# 2
tree = treelib.parse_newick("((a,a),b);")
recon = phylo.reconcile(tree, stree, gene2species)
p = birthDeathCount(2, T, duprate, lossrate) * b
p2 = exp(calcBirthDeathPrior(tree, stree, recon, duprate, lossrate))
p2 *= numRedunantTopology(tree.root, gene2species)
print p, p2
fequal(p, p2)
# 3
tree = treelib.parse_newick("(((a,a),a),b);")
recon = phylo.reconcile(tree, stree, gene2species)
p = birthDeathCount(3, T, duprate, lossrate) * b
p2 = exp(calcBirthDeathPrior(tree, stree, recon, duprate, lossrate))
p2 *= numRedunantTopology(tree.root, gene2species)
print p, p2
fequal(p, p2)
# 4
tree = treelib.parse_newick("(((a,a),(a,a)),b);")
recon = phylo.reconcile(tree, stree, gene2species)
p = birthDeathCount(4, T, duprate, lossrate) * b / 3.0
p2 = exp(calcBirthDeathPrior(tree, stree, recon, duprate, lossrate))
p2 *= numRedunantTopology(tree.root, gene2species)
print p, p2
fequal(p, p2)
def do_test_birth_death_gene_sim(self, stree, gene2species,
duprate, lossrate,
ntrees=10000, tabsize=30):
"""Perform a birth death gene tree simulation test"""
doomtable = calcDoomTable(stree, duprate, lossrate)
tops = []
lookup = {}
def rename_tree(tree, gene2species):
if len(tree.nodes) == 0:
return
spcounts = util.hist_dict(map(gene2species, tree.leaf_names()))
names = {}
for sp, c in spcounts.items():
names[sp] = range(1, c+1)
random.shuffle(names[sp])
for node in tree.leaves():
sp = gene2species(node.name)
tree.rename(node.name, sp + "." + str(names[sp].pop()))
util.tic("simulating %d trees" % ntrees)
for i in xrange(ntrees):
tree, recon, events = birthdeath.sample_birth_death_gene_tree(
stree, duprate, lossrate,
removeloss=True)
phylo.add_implied_spec_nodes(tree, stree, recon, events)
if len(tree.nodes) == 1 and recon[tree.root] == stree.root:
tops.append("()")
lookup["()"] = (None, None, None)
else:
rename_tree(tree, gene2species)
tops.append(phylo.hash_tree(tree))
lookup[tops[-1]] = (tree, recon, events)
util.toc()
hist = histtab(tops)
probs = []
for row in hist:
tree, recon, events = lookup[row["item"]]
if tree is None:
probs.append(exp(doomtable[-1]))
else:
p = c_calcBirthDeathPrior(tree, stree, recon,
duprate, lossrate,
events=events)
p2 = calcBirthDeathPrior(tree, stree, recon,
duprate, lossrate,
events=events)
fequal(p, p2)
probs.append(exp(p))
return hist, probs