Example #1
0
    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()
Example #2
0
    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()
Example #3
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()
Example #4
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()