def sample_arg_mutations(arg, mu, times=None):
"""
Simulate mutations on an ARG.
Mutations are represented as (node, parent, site, time).
arg -- ARG on which to simulate mutations
mu -- mutation rate (mutations/site/gen)
times -- optional list of discretized time points
"""
mutations = []
minlen = times[1] * .1 if times else 0.0
for (start, end), tree in arglib.iter_tree_tracks(arg):
arglib.remove_single_lineages(tree)
for node in tree:
if not node.parents:
continue
blen = max(node.get_dist(), minlen)
rate = blen * mu
i = start
while i < end:
i += random.expovariate(rate)
if i < end:
t = random.uniform(node.age, node.age + blen)
mutations.append((node, node.parents[0], int(i), t))
return mutations
def sample_arg_mutations(arg, mu, times=None):
"""
Simulate mutations on an ARG.
Mutations are represented as (node, parent, site, time).
arg -- ARG on which to simulate mutations
mu -- mutation rate (mutations/site/gen)
times -- optional list of discretized time points
"""
mutations = []
minlen = times[1] * 0.1 if times else 0.0
for (start, end), tree in arglib.iter_tree_tracks(arg):
arglib.remove_single_lineages(tree)
for node in tree:
if not node.parents:
continue
blen = max(node.get_dist(), minlen)
rate = blen * mu
i = start
while i < end:
i += random.expovariate(rate)
if i < end:
t = random.uniform(node.age, node.age + blen)
mutations.append((node, node.parents[0], int(i), t))
return mutations
def test_arg_equal(arg, arg2):
# test recomb points
recombs = sorted(x.pos for x in arg if x.event == "recomb")
recombs2 = sorted(x.pos for x in arg2 if x.event == "recomb")
assert recombs == recombs2
# check local tree topologies
for (start, end), tree in arglib.iter_tree_tracks(arg):
pos = (start + end) / 2.0
arglib.remove_single_lineages(tree)
tree1 = tree.get_tree()
tree2 = arg2.get_marginal_tree(pos)
arglib.remove_single_lineages(tree2)
tree2 = tree2.get_tree()
hash1 = phylo.hash_tree(tree1)
hash2 = phylo.hash_tree(tree2)
print
print pos
print hash1
print hash2
assert hash1 == hash2
# check sprs
sprs1 = arglib.iter_arg_sprs(arg, use_leaves=True)
sprs2 = arglib.iter_arg_sprs(arg2, use_leaves=True)
for (pos1, recomb1, coal1), (pos2, recomb2, coal2) in izip(sprs1, sprs2):
recomb1 = (sorted(recomb1[0]), recomb1[1])
recomb2 = (sorted(recomb2[0]), recomb2[1])
coal1 = (sorted(coal1[0]), coal1[1])
coal2 = (sorted(coal2[0]), coal2[1])
print
print (pos1, recomb1, coal1)
print (pos2, recomb2, coal2)
# check pos, leaves, time
assert pos1 == pos2
assert recomb1 == recomb2
assert coal1 == coal2
def test_arg_equal(arg, arg2):
# test recomb points
recombs = sorted(x.pos for x in arg if x.event == "recomb")
recombs2 = sorted(x.pos for x in arg2 if x.event == "recomb")
assert recombs == recombs2
# check local tree topologies
for (start, end), tree in arglib.iter_tree_tracks(arg):
pos = (start + end) / 2.0
arglib.remove_single_lineages(tree)
tree1 = tree.get_tree()
tree2 = arg2.get_marginal_tree(pos)
arglib.remove_single_lineages(tree2)
tree2 = tree2.get_tree()
hash1 = phylo.hash_tree(tree1)
hash2 = phylo.hash_tree(tree2)
print
print pos
print hash1
print hash2
assert hash1 == hash2
# check sprs
sprs1 = arglib.iter_arg_sprs(arg, use_leaves=True)
sprs2 = arglib.iter_arg_sprs(arg2, use_leaves=True)
for (pos1, recomb1, coal1), (pos2, recomb2, coal2) in izip(sprs1, sprs2):
recomb1 = (sorted(recomb1[0]), recomb1[1])
recomb2 = (sorted(recomb2[0]), recomb2[1])
coal1 = (sorted(coal1[0]), coal1[1])
coal2 = (sorted(coal2[0]), coal2[1])
print
print(pos1, recomb1, coal1)
print(pos2, recomb2, coal2)
# check pos, leaves, time
assert pos1 == pos2
assert recomb1 == recomb2
assert coal1 == coal2
def test_thread(self):
"""
Test thread retrieval
"""
k = 10
n = 1e4
rho = 1.5e-8 * 10
mu = 2.5e-8 * 100
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
for (block, tree), threadi in izip(
arglib.iter_tree_tracks(arg),
arghmm.iter_chrom_thread(arg, arg["n9"], by_block=True)):
print block
print threadi
treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)
def test_thread(self):
"""
Test thread retrieval
"""
k = 10
n = 1e4
rho = 1.5e-8 * 10
mu = 2.5e-8 * 100
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
for (block, tree), threadi in izip(
arglib.iter_tree_tracks(arg),
arghmm.iter_chrom_thread(arg, arg["n9"], by_block=True)):
print block
print threadi
treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)
def test_est_popsize2(self):
"""
Fully sample an ARG from stratch using API
"""
k = 20
rho = 1.5e-8
mu = 2.5e-8
length = int(4e6)
popsize = 1e4
popsize2 = 1e4 * .5
a = int(.3 * length)
b = int(.7 * length)
refine = 0
util.tic("sim ARG")
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=0, end=a)
arg = arglib.sample_arg_smc(k, 2 * popsize2,
rho, start=a, end=b,
init_tree=arg)
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=b, end=length,
init_tree=arg)
util.toc()
x = []; y = []
for (start, end), tree in arglib.iter_tree_tracks(arg):
arglib.remove_single_lineages(tree)
x.append(start)
y.append(mle_popsize_tree(tree, mintime=0))
x2, y2 = stats.smooth2(x, y, 100e3)
p = plot(x, y, ymin=0)
p.plot(x2, y2, style='lines')
p.plot([0, a, a, b, b, length],
[popsize, popsize, popsize2, popsize2, popsize, popsize],
style='lines')
pause()
def test_est_popsize2(self):
"""
Fully sample an ARG from stratch using API
"""
k = 20
rho = 1.5e-8
mu = 2.5e-8
length = int(4e6)
popsize = 1e4
popsize2 = 1e4 * .5
a = int(.3 * length)
b = int(.7 * length)
refine = 0
util.tic("sim ARG")
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=0, end=a)
arg = arglib.sample_arg_smc(k, 2 * popsize2,
rho, start=a, end=b,
init_tree=arg)
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=b, end=length,
init_tree=arg)
util.toc()
x = []; y = []
for (start, end), tree in arglib.iter_tree_tracks(arg):
arglib.remove_single_lineages(tree)
x.append(start)
y.append(mle_popsize_tree(tree, mintime=0))
x2, y2 = stats.smooth2(x, y, 100e3)
p = plot(x, y, ymin=0)
p.plot(x2, y2, style='lines')
p.plot([0, a, a, b, b, length],
[popsize, popsize, popsize2, popsize2, popsize, popsize],
style='lines')
pause()
if abs(times3[i] - x) < 1:
times.append(times3[i])
elif abs(times3[j] - x) < 1:
times.append(times3[j])
else:
times.append(x)
return times
#=============================================================================
if 1:
#times = arghmm.get_time_points(ntimes=20)
arg = arglib.read_arg("test/data/sample.arg")
seqs = read_fasta("test/data/sample.fa")
trees = list(arglib.iter_tree_tracks(arg, convert=True))
# draw mappings
win = argvis.show_tree_track(trees)
nleaves = ilen(arg.leaves())
for i in xrange(len(trees)-1):
block1, _tree1 = trees[i]
block2, _tree2 = trees[i + 1]
pos = block2[0]
tree1 = arg.get_marginal_tree(pos-.5)
tree2 = arg.get_marginal_tree(pos+.5)
layout1 = argvis.layout_arg(tree1)
layout2 = argvis.layout_arg(tree2)
#layout1 = treelib.layout_tree_vertical(
# treelib.layout_tree(tree1, xscale=1, yscale=1), leaves=0)
def test_est_arg_popsize(self):
"""
Fully sample an ARG from stratch using API
"""
k = 20
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(2e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
popsize = 1e4
popsize2 = 1e4 * .5
a = int(.3 * length)
b = int(.7 * length)
refine = 0
util.tic("sim ARG")
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=0, end=a)
arg = arglib.sample_arg_smc(k, 2 * popsize2,
rho, start=a, end=b,
init_tree=arg)
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=b, end=length,
init_tree=arg)
# sim seq
mut = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, mut)
util.toc()
# sample arg
util.tic("sample arg")
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=1e4, carg=True)
arg2 = arghmm.resample_climb_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
arg2 = arghmm.resample_all_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
util.toc()
x = []; y = []
for (start, end), tree in arglib.iter_tree_tracks(arg2):
arglib.remove_single_lineages(tree)
x.append(start)
y.append(mle_popsize_tree(tree, mintime=0))
# thin popsizes
x2 = list(range(0, length, length//5000)); y2 = []
j = 0
for i in range(len(x2)):
while j < len(x) and x[j] < x2[i]:
j += 1
y2.append(y[min(j, len(y)-1)])
x3, y3 = stats.smooth2(x2, y2, 100e3)
p = plot(x, y, ymin=0)
p.plot(x3, y3, style='lines')
p.plot([0, a, a, b, b, length],
[popsize, popsize, popsize2, popsize2, popsize, popsize],
style='lines')
pause()
if abs(times3[i] - x) < 1:
times.append(times3[i])
elif abs(times3[j] - x) < 1:
times.append(times3[j])
else:
times.append(x)
return times
#=============================================================================
if 1:
#times = arghmm.get_time_points(ntimes=20)
arg = arglib.read_arg("test/data/sample.arg")
seqs = read_fasta("test/data/sample.fa")
trees = list(arglib.iter_tree_tracks(arg, convert=True))
# draw mappings
win = argvis.show_tree_track(trees)
nleaves = ilen(arg.leaves())
for i in xrange(len(trees) - 1):
block1, _tree1 = trees[i]
block2, _tree2 = trees[i + 1]
pos = block2[0]
tree1 = arg.get_marginal_tree(pos - .5)
tree2 = arg.get_marginal_tree(pos + .5)
layout1 = argvis.layout_arg(tree1)
layout2 = argvis.layout_arg(tree2)
#layout1 = treelib.layout_tree_vertical(
# treelib.layout_tree(tree1, xscale=1, yscale=1), leaves=0)
def test_est_arg_popsize(self):
"""
Fully sample an ARG from stratch using API
"""
k = 20
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(2e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
popsize = 1e4
popsize2 = 1e4 * .5
a = int(.3 * length)
b = int(.7 * length)
refine = 0
util.tic("sim ARG")
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=0, end=a)
arg = arglib.sample_arg_smc(k, 2 * popsize2,
rho, start=a, end=b,
init_tree=arg)
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=b, end=length,
init_tree=arg)
# sim seq
mut = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, mut)
util.toc()
# sample arg
util.tic("sample arg")
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=1e4, carg=True)
arg2 = arghmm.resample_climb_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
arg2 = arghmm.resample_all_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
util.toc()
x = []; y = []
for (start, end), tree in arglib.iter_tree_tracks(arg2):
arglib.remove_single_lineages(tree)
x.append(start)
y.append(mle_popsize_tree(tree, mintime=0))
# thin popsizes
x2 = range(0, length, length//5000); y2 = []
j = 0
for i in range(len(x2)):
while j < len(x) and x[j] < x2[i]:
j += 1
y2.append(y[min(j, len(y)-1)])
x3, y3 = stats.smooth2(x2, y2, 100e3)
p = plot(x, y, ymin=0)
p.plot(x3, y3, style='lines')
p.plot([0, a, a, b, b, length],
[popsize, popsize, popsize2, popsize2, popsize, popsize],
style='lines')
pause()
