def prob_locus_coal_recon_topology(tree, recon, locus_tree, n, daughters):
"""
Returns the log probability of a reconciled gene tree ('tree', 'recon')
from the coalescent model given a locus tree 'locus_tree',
population sizes 'n', and daughters set 'daughters'
"""
# initialize popsizes, lineage counts, and divergence times
popsizes = coal.init_popsizes(locus_tree, n)
lineages = coal.count_lineages_per_branch(tree, recon, locus_tree)
locus_times = treelib.get_tree_timestamps(locus_tree)
# calc log probability
lnp = coal.pmrt(
tree, recon, locus_tree, popsizes, lineages=lineages)
def walk(node, gene_counts, leaves):
if node.is_leaf():
gene_counts[node.name] = lineages[node][0]
leaves.add(node)
else:
for child in node.children:
if child in daughters:
gene_counts[child.name] = 1
leaves.add(child)
else:
walk(child, gene_counts, leaves)
for daughter in daughters:
# determine leaves of the coal subtree
gene_counts = {}
leaves = set()
walk(daughter, gene_counts, leaves)
p = coal.cdf_mrca_bounded_multicoal(
gene_counts, locus_times[daughter.parent], locus_tree, popsizes,
sroot=daughter, sleaves=leaves, stimes=locus_times)
if p == -util.INF:
return -util.INF
lnp -= p
return lnp
def show_coal_track2(tree_track):
win = summon.Window()
bgcolor = (1, 1, 1, .1)
cmap = util.rainbow_color_map(low=0.0, high=1.0)
tracks = {}
maxage = 0
for (start, end), tree in tree_track:
print start
l = []
times = treelib.get_tree_timestamps(tree)
nleaves = len(tree.leaves())
maxage2 = 0
for node in tree:
if len(node.children) > 1:
age = times[node]
freq = len(node.leaves()) / float(nleaves)
#sizes = [len(x.leaves()) for x in node.children]
#m = max(sizes)
#n = sum(sizes)
#pval = 2 * (n - m) / float(n - 1)
l.extend([color(*cmap.get(freq)), start, age, end, age])
if age > maxage2:
maxage2 = age
win.add_group(group(lines(*l), color(*bgcolor),
box(start, 0, end, maxage2, fill=True)))
if maxage2 > maxage:
maxage = maxage2
def func():
x, y = win.get_mouse_pos()
print "pos=%s age=%f" % (util.int2pretty(int(x)), y)
win.add_group(hotspot("click", 0, 0, end, maxage,
func))
win.home("exact")
return win
def show_coal_track2(tree_track):
win = summon.Window()
bgcolor = (1, 1, 1, .1)
cmap = util.rainbow_color_map(low=0.0, high=1.0)
tracks = {}
maxage = 0
for (start, end), tree in tree_track:
print(start)
l = []
times = treelib.get_tree_timestamps(tree)
nleaves = len(tree.leaves())
maxage2 = 0
for node in tree:
if len(node.children) > 1:
age = times[node]
freq = len(node.leaves()) / float(nleaves)
#sizes = [len(x.leaves()) for x in node.children]
#m = max(sizes)
#n = sum(sizes)
#pval = 2 * (n - m) / float(n - 1)
l.extend([color(*cmap.get(freq)), start, age, end, age])
if age > maxage2:
maxage2 = age
win.add_group(group(lines(*l), color(*bgcolor),
box(start, 0, end, maxage2, fill=True)))
if maxage2 > maxage:
maxage = maxage2
def func():
x, y = win.get_mouse_pos()
print("pos=%s age=%f" % (util.int2pretty(int(x)), y))
win.add_group(hotspot("click", 0, 0, end, maxage,
func))
win.home("exact")
return win
def test_cdf_bmc(self):
# test cdf mrca BMC
stree = treelib.parse_newick(
"((A:1000, B:1000):500, (C:700, D:700):800);")
n = 1000
gene_counts = dict.fromkeys(stree.leaf_names(), 1)
T = 2000
p = exp(coal.cdf_mrca_bounded_multicoal(gene_counts, T, stree, n))
nsamples = 5000
c = 0
for i in xrange(nsamples):
tree, recon = coal.sample_multicoal_tree(stree, n)
if treelib.get_tree_timestamps(tree)[tree.root] < T:
c += 1
p2 = c / float(nsamples)
fequal(p, p2, .05)
def prob_locus_coal_recon_topology(tree, recon, locus_tree, n, daughters):
ptree, nodes, nodelookup = dlcoal.make_ptree(tree)
pltree, lnodes, lnodelookup = dlcoal.make_ptree(locus_tree)
recon2 = dlcoal.make_recon_array(tree, recon, nodes, lnodelookup)
popsizes = compbio.coal.init_popsizes(locus_tree, n)
popsizes2 = [popsizes[lnode.name] for lnode in lnodes]
ltimes = treelib.get_tree_timestamps(locus_tree)
ltimes2 = [ltimes[lnode] for lnode in lnodes]
daughters2 = [lnodelookup[lnode] for lnode in daughters]
p = dlcoal.dlcoalc.prob_locus_coal_recon_topology(
c_list(c_int, ptree), len(nodes), c_list(c_int, recon2),
c_list(c_int, pltree), 0, len(lnodes),
c_list(c_double, popsizes2), c_list(c_double, ltimes2),
c_list(c_int, daughters2), len(daughters))
return p
def dlcoal_sims(outdir, nsims, stree, n, duprate, lossrate,
start=0,
freq=1.0, freqdup=.05, freqloss=.05, steptime=None,
nsteps=100,
full_log=False,
**options):
if steptime is None:
stimes = treelib.get_tree_timestamps(stree)
steptime = stimes[stree.root] / float(nsteps)
for i in xrange(start, nsims):
outfile = phylo.phylofile(outdir, str(i), "")
util.makedirs(os.path.dirname(outfile))
print "simulating", outfile
# sample a new tree from DLCoal model
coal_tree, ex = sample_dlcoal_hem(
stree, n, duprate, lossrate,
freq, freqdup, freqloss, steptime,
keep_extinct=full_log,
**options)
# write datastructures
dlcoal.write_dlcoal_recon(outfile, coal_tree, ex)
if full_log:
full_logfile = phylo.phylofile(outdir, str(i), ".locus.info")
full_locus_tree = ex["full_locus_tree"]
ex2 = generate_extras(stree, full_locus_tree)
daughters = ex2["daughters"]
out = open(full_logfile, "w")
out.write("hem\t%d\n" %
int(is_locus_tree_hemiplasy(full_locus_tree, daughters)))
out.close()
def sample_multilocus_tree(stree, n, leaf_counts=None,
daughters=set(),
namefunc=None):
"""
Returns a gene tree from a multilocus coalescent process
n -- population size (int or dict)
If n is a dict it must map from species name to population size
"""
# initialize vector for how many genes per extant species
if leaf_counts is None:
leaf_counts = dict((l, 1) for l in stree.leaf_names())
# initialize function for generating new gene names
if namefunc is None:
spcounts = dict((l, 1) for l in stree.leaf_names())
def namefunc(sp):
name = sp + "_" + str(spcounts[sp])
spcounts[sp] += 1
return name
stimes = treelib.get_tree_timestamps(stree)
# initialize population sizes
popsizes = coal.init_popsizes(stree, n)
# init gene counts
counts = dict((n.name, 0) for n in stree)
counts.update(leaf_counts)
# init lineage counts
lineages = {stree.root: [None, None]}
for node in stree.leaves():
lineages[node] = [leaf_counts[node.name], None]
for node in daughters:
if node not in lineages:
lineages[node] = [None, 1]
else:
lineages[node][1] = 1
def get_subtree(node, leaves, leaf_counts2):
"""collects info of subtree rooted at node"""
if node.is_leaf():
leaves.add(node)
leaf_counts2[node.name] = leaf_counts[node.name]
else:
for child in node.children:
if child in daughters:
leaves.add(child)
leaf_counts2[child.name] = 1
else:
get_subtree(child, leaves, leaf_counts2)
# loop through subtrees
for snode in chain(daughters, [stree.root]):
# determine leaves of the coal subtree
leaves = set()
leaf_counts2 = {}
get_subtree(snode, leaves, leaf_counts2)
if snode.parent:
T = stimes[snode.parent]
else:
T = None
# calc table
prob_counts = coal.calc_prob_counts_table(
leaf_counts2, T, stree, popsizes,
sroot=snode, sleaves=leaves, stimes=stimes)
# sample lineage counts
try:
coal.sample_lineage_counts(snode, leaves, popsizes, stimes, T,
lineages, prob_counts)
except:
print snode.name
treelib.draw_tree_names(stree, maxlen=8)
util.print_dict(lineages, key=lambda x: x.name)
raise
# sample coal times
tree, recon = coal.coal_cond_lineage_counts(
lineages, stree.root, set(stree.leaves()),
popsizes, stimes, None, namefunc)
return tree, recon
def prob_dlcoal_recon_topology(coal_tree, coal_recon,
locus_tree, locus_recon, locus_events,
daughters,
stree, n, duprate, lossrate,
pretime=None, premean=None,
nsamples=100,
add_spec=True, info=None):
"""
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
"""
# 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
dl_prob = duploss.prob_dup_loss(
locus_tree, stree, locus_recon, locus_events,
duprate, lossrate)
# daughters probability
dups = phylo.count_dup(locus_tree, locus_events)
d_prob = dups * log(.5)
# integrate over duplication times using sampling
stimes = treelib.get_tree_timestamps(stree)
prob = 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)
# logging info
if info is not None:
info["duploss_prob"] = dl_prob
info["daughters_prob"] = d_prob
info["coal_prob"] = prob
info["prob"] = dl_prob + d_prob + prob - log(nsamples)
return dl_prob + d_prob + prob - log(nsamples)
def sample_dup_times(tree, stree, recon, birth, death,
pretime=None, premean=None, events=None):
"""
Sample duplication times for a gene tree in the dup-loss model
"""
if events is None:
events = phylo.label_events(tree, recon)
# get species tree timestamps
stimes = treelib.get_tree_timestamps(stree)
#treelib.check_timestamps(stree, stimes)
# init timestamps for gene tree
times = {}
# set pretimes
if events[tree.root] != "spec":
if recon[tree.root] != stree.root:
# tree root is a dup within species tree
snode = recon[tree.root]
start_time = stimes[snode.parent]
time_span = start_time - stimes[snode]
else:
# tree root is a pre-spec dup
if pretime is None:
if premean is None:
raise Exception("must set pre-mean")
pretime = 0.0
while pretime == 0.0:
pretime = random.expovariate(1/premean)
start_time = stimes[stree.root] + pretime
time_span = pretime
sample_dup_times_subtree(times, start_time, time_span, tree.root,
recon, events,
stree, birth, death)
# set times
for node in tree.preorder():
if events[node] == "spec":
# set speciation time
times[node] = stimes[recon[node]]
elif (events[node] == "dup" and
node.parent is not None and
recon[node] != recon[node.parent]):
# set duplication times within duplication subtree
# node is duproot
snode = recon[node]
start_time = stimes[snode.parent]
time_span = start_time - stimes[snode]
sample_dup_times_subtree(times, start_time, time_span,
node,
recon, events,
stree, birth, death)
elif events[node] == "gene":
times[node] = 0.0
return times
def sample_dup_times(tree, stree, recon, birth, death, pretime=None, premean=None, events=None):
"""
Sample duplication times for a gene tree in the dup-loss model
NOTE: Implied speciation nodes must be present
"""
def gene2species(gene):
return recon[tree.nodes[gene]].name
if events is None:
events = phylo.label_events(tree, recon)
# get species tree timestamps
stimes = treelib.get_tree_timestamps(stree)
# treelib.check_timestamps(stree, stimes)
# init timestamps for gene tree
times = {}
# set pretimes
if events[tree.root] != "spec":
if recon[tree.root] != stree.root:
# tree root is a dup within species tree
snode = recon[tree.root]
start_time = stimes[snode.parent]
time_span = snode.dist
if recon[tree.root] == stree.root:
# tree root is a pre-spec dup
if pretime is None:
if premean is None:
raise Exception("must set pre-mean")
pretime = 0.0
while pretime == 0.0:
pretime = random.expovariate(1 / premean)
start_time = stimes[stree.root] + pretime
time_span = pretime
sample_dup_times_subtree(times, start_time, time_span, tree.root, recon, events, stree, birth, death)
# set times
for node in tree.preorder():
if events[node] == "spec":
# set speciation time
start_time = times[node] = stimes[recon[node]]
if node.parent:
if times[node] > times[node.parent]:
print "bad", node.name
# raise Exception("bad time")
# set duplication times within duplication subtree
for duproot in node.children:
if events[duproot] == "dup":
snode = recon[duproot]
time_span = snode.dist
# assert start_time - time_span >= stimes[snode], \
# (duproot.name, start_time, time_span, stimes[snode])
sample_dup_times_subtree(times, start_time, time_span, duproot, recon, events, stree, birth, death)
elif events[node] == "gene":
times[node] = 0.0
return times
def sample_dup_times(tree,
stree,
recon,
birth,
death,
pretime=None,
premean=None,
events=None):
"""
Sample duplication times for a gene tree in the dup-loss model
NOTE: Implied speciation nodes must be present
"""
def gene2species(gene):
return recon[tree.nodes[gene]].name
if events is None:
events = phylo.label_events(tree, recon)
# get species tree timestamps
stimes = treelib.get_tree_timestamps(stree)
#treelib.check_timestamps(stree, stimes)
# init timestamps for gene tree
times = {}
# set pretimes
if events[tree.root] != "spec":
if recon[tree.root] != stree.root:
# tree root is a dup within species tree
snode = recon[tree.root]
start_time = stimes[snode.parent]
time_span = snode.dist
if recon[tree.root] == stree.root:
# tree root is a pre-spec dup
if pretime is None:
if premean is None:
raise Exception("must set pre-mean")
pretime = 0.0
while pretime == 0.0:
pretime = random.expovariate(1 / premean)
start_time = stimes[stree.root] + pretime
time_span = pretime
sample_dup_times_subtree(times, start_time, time_span, tree.root,
recon, events, stree, birth, death)
# set times
for node in tree.preorder():
if events[node] == "spec":
# set speciation time
start_time = times[node] = stimes[recon[node]]
if node.parent:
if times[node] > times[node.parent]:
print "bad", node.name
#raise Exception("bad time")
# set duplication times within duplication subtree
for duproot in node.children:
if events[duproot] == "dup":
snode = recon[duproot]
time_span = snode.dist
#assert start_time - time_span >= stimes[snode], \
# (duproot.name, start_time, time_span, stimes[snode])
sample_dup_times_subtree(times, start_time, time_span,
duproot, recon, events, stree,
birth, death)
elif events[node] == "gene":
times[node] = 0.0
return times
lossrate = 0.12 # events/lineages/myr
gentime = 0.1 # yr / gen
popsizes = 2 * 1e6 * gentime / 1e6 # "normalized popsize" = 2 (diploid) * Ne * yr/gen * myr/yr (first 1e6 is the pop size)
subrate = 5e-9 / gentime * 1e6 # sub/site/myr = sub/site/gen * gen/yr * yr/myr\
rates, freqs, alphas = pllprob.optimize_parameters(alnfile,
partfile,
coal_tree_treefix,
threads=1,
seed=ALIGNMENT_SEED,
eps=1)
nsamples_coal = 1
nsamples_locus = 1
times = treelib.get_tree_timestamps(stree)
pretime = None
premean = 0.5 * times[stree.root]
p_raxml = prob_locus_gene_species_alignment_recon(alnfile,
partfile,
stree,
popsizes,
duprate,
lossrate,
subrate,
pretime,
premean,
coal_tree_raxml,
coal_recon_raxml,
nsamples_coal,