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()