def test_sample_arg_popsizes_trees(self):
"""
Fully sample an ARG from stratch using API
"""
k = 2
rho = 1.5e-8
mu = 2.5e-8
length = int(20e6)
times = arghmm.get_time_points(ntimes=30, maxtime=160000)
popsizes = [1e4 * (61.-i)/60. for i in range(len(times))]
#popsizes = [1e4 for i in range(len(times))]
refine = 0
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()
util.tic("estimate popsizes")
popsizes2 = arghmm.est_popsizes_trees(arg, times=times,
step=length/1000, verbose=True)
util.toc()
print(popsizes2)
p = plot(times, popsizes, xlog=10, xmin=10, ymin=0, ymax=20000)
p.plot(times[1:], popsizes2)
pause()
def test_sample_arg_popsizes_trees(self):
"""
Fully sample an ARG from stratch using API
"""
k = 2
rho = 1.5e-8
mu = 2.5e-8
length = int(20e6)
times = arghmm.get_time_points(ntimes=30, maxtime=160000)
popsizes = [1e4 * (61.-i)/60. for i in range(len(times))]
#popsizes = [1e4 for i in range(len(times))]
refine = 0
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()
util.tic("estimate popsizes")
popsizes2 = arghmm.est_popsizes_trees(arg, times=times,
step=length/1000, verbose=True)
util.toc()
print popsizes2
p = plot(times, popsizes, xlog=10, xmin=10, ymin=0, ymax=20000)
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_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()
