def test_sample_arg_popsizes_trees_infer(self):
"""
Fully sample an ARG from stratch using API
"""
k = 6
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=160000)
popsizes = [1e4 * (61.-i)/60. for i in range(len(times))]
refine = 5
util.tic("sim ARG")
#arg = arglib.sample_arg_smc(k, 2 * popsizes[0],
# rho, start=0, end=length)
arg = arghmm.sample_arg_dsmc(k, [2*p for p in popsizes],
rho, start=0, end=length, times=times)
util.toc()
muts = arghmm.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
popsizes2 = [0] * (len(times) - 1)
nsamples = 1
for i in range(nsamples):
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=popsizes,
refine=refine, verbose=True, carg=True)
popsizes3 = arghmm.est_popsizes_trees(arg2, times, length/1000,
verbose=True)
print(popsizes3)
popsizes2 = vadd(popsizes2, popsizes3)
popsizes2 = vdivs(popsizes2, float(nsamples))
print(popsizes2)
p = plot(times, popsizes, xlog=10, xmin=10)
p.plot(times[1:], popsizes2)
pause()
def test_sample_arg_popsizes_trees_infer(self):
"""
Fully sample an ARG from stratch using API
"""
k = 6
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=160000)
popsizes = [1e4 * (61.-i)/60. for i in range(len(times))]
refine = 5
util.tic("sim ARG")
#arg = arglib.sample_arg_smc(k, 2 * popsizes[0],
# rho, start=0, end=length)
arg = arghmm.sample_arg_dsmc(k, [2*p for p in popsizes],
rho, start=0, end=length, times=times)
util.toc()
muts = arghmm.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
popsizes2 = [0] * (len(times) - 1)
nsamples = 1
for i in range(nsamples):
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=popsizes,
refine=refine, verbose=True, carg=True)
popsizes3 = arghmm.est_popsizes_trees(arg2, times, length/1000,
verbose=True)
print popsizes3
popsizes2 = vadd(popsizes2, popsizes3)
popsizes2 = vdivs(popsizes2, float(nsamples))
print popsizes2
p = plot(times, popsizes, xlog=10, xmin=10)
p.plot(times[1:], popsizes2)
pause()
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()
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()
