def test_coin_sample_post(self):
        """Test sampling from posterior distribution"""

        outdir = 'test/tmp/test_hmm/test_coin_sample_post/'
        make_clean_dir(outdir)
        model = make_coin_model()

        # sample states and data
        ndata = 100
        states = list(islice(hmm.sample_hmm_states(model), ndata))
        data = list(hmm.sample_hmm_data(model, states))
        model.prob_emission = (lambda pos, state:
                               model.prob_emission_data(state, data[pos]))

        p = Gnuplot()
        p.enableOutput(False)
        p.plot(states, style="lines")

        probs = hmm.get_posterior_probs(model, len(data))
        states2 = [exp(probs[i][1]) for i in xrange(len(data))]
        p.plot(util.vadds(states2, 1.5), style="lines", miny=-1, maxy=12)

        for i in range(2, 10):
            states2 = hmm.sample_posterior(model, ndata)
            self.assertTrue(stats.corr(states, states2) > .5)

            p.plot(util.vadds(states2, 1.5*i), style="lines", miny=-1, maxy=12)
        p.enableOutput(True)
        p.save(outdir + 'plot.png')
Example #2
0
def test_trans():
    """
    Calculate transition probabilities
    """
    create_data = False
    if create_data:
        make_clean_dir('test/data/test_trans')

    k = 8
    n = 1e4
    rho = 1.5e-8 * 20
    length = 1000
    times = argweaver.get_time_points(ntimes=10, maxtime=200000)
    popsizes = [n] * len(times)
    ntests = 40

    # generate test data
    if create_data:
        for i in range(ntests):
            arg = arglib.sample_arg(k, 2*n, rho, start=0, end=length)
            argweaver.discretize_arg(arg, times)
            arg.write('test/data/test_trans/%d.arg' % i)

    for i in range(ntests):
        print 'arg', i
        arg = arglib.read_arg('test/data/test_trans/%d.arg' % i)
        argweaver.discretize_arg(arg, times)
        pos = 10
        tree = arg.get_marginal_tree(pos)

        assert argweaverc.assert_transition_probs(tree, times, popsizes, rho)
Example #3
0
    def test_coin_sample_post(self):
        """Test sampling from posterior distribution"""

        outdir = 'test/tmp/test_hmm/test_coin_sample_post/'
        make_clean_dir(outdir)
        model = make_coin_model()

        # sample states and data
        ndata = 100
        states = list(islice(hmm.sample_hmm_states(model), ndata))
        data = list(hmm.sample_hmm_data(model, states))
        model.prob_emission = (
            lambda pos, state: model.prob_emission_data(state, data[pos]))

        p = Gnuplot()
        p.enableOutput(False)
        p.plot(states, style="lines")

        probs = hmm.get_posterior_probs(model, len(data))
        states2 = [exp(probs[i][1]) for i in xrange(len(data))]
        p.plot(util.vadds(states2, 1.5), style="lines", miny=-1, maxy=12)

        for i in range(2, 10):
            states2 = hmm.sample_posterior(model, ndata)
            self.assertTrue(stats.corr(states, states2) > .5)

            p.plot(util.vadds(states2, 1.5 * i),
                   style="lines",
                   miny=-1,
                   maxy=12)
        p.enableOutput(True)
        p.save(outdir + 'plot.png')
Example #4
0
    def test_cdf_coal_cond_counts(self):

        # test coalescent pdf when conditioned on future lineage counts

        outdir = 'test/tmp/test_coal/Coal_test_cdf_coal_cond_counts/'
        make_clean_dir(outdir)

        a = 5
        for b in xrange(2, a):
            t = 500
            n = 1000
            p = Gnuplot()
            p.enableOutput(False)
            p.plotfunc(lambda x: coal.cdf_coal_cond_counts(
                x, a, b, t, n), 0, t, 10)

            # draw single coal samples using rejection sampling
            s = []
            for i in xrange(1000):
                while True:
                    times = coal.sample_coal_times(a, n)
                    if times[a-b-1] < t and (b == 1 or times[a-b] > t):
                        break
                s.append(times[0])

            x2, y2 = stats.cdf(s)
            p.plot(x2, y2, style='lines')
            p.enableOutput(True)
            p.save(outdir + 'plot-%d.png' % b)

            eq_sample_pdf(
                x2, lambda x: coal.prob_coal_cond_counts(x, a, b, t, n), 40)
Example #5
0
    def test2(self):
        outdir = 'test/tmp/test_vistrans/Vis_test2/'
        make_clean_dir(outdir)

        stree = treelib.parse_newick(stree_newick)
        tree = treelib.read_tree(treefile2)
        brecon = phylo.read_brecon(breconfile2, tree, stree)

        transsvg.draw_tree(tree, brecon, stree, filename=outdir + "tree.svg")
    def test2(self):
        outdir = 'test/tmp/test_vistrans/Vis_test2/'
        make_clean_dir(outdir)

        stree = treelib.parse_newick(stree_newick)
        tree = treelib.read_tree(treefile2)
        brecon = phylo.read_brecon(breconfile2, tree, stree)

        transsvg.draw_tree(tree, brecon, stree, filename=outdir + "tree.svg")
Example #7
0
def test_install():
    """
    Test installing compbio.
    """

    make_clean_dir("test/tmp/install")
    run_cmd("python setup.py clean > /dev/null")
    run_cmd("python setup.py install --prefix=test/tmp/install > /dev/null")
    assert os.path.exists("test/tmp/install/bin/viewtree")
Example #8
0
def test_install():
    """
    Test installing ARGweaver.
    """

    make_clean_dir("test/tmp/install")
    run_cmd("python setup.py clean > /dev/null")
    run_cmd("make install prefix=test/tmp/install > /dev/null")
    run_cmd("PYTHONPATH=test/tmp/install python -c 'import argweaver'")
    assert os.path.exists("test/tmp/install/bin/arg-sample")
Example #9
0
def test_install():
    """
    Test installing ARGweaver.
    """

    make_clean_dir("test/data/install")
    run_cmd("python setup.py clean > /dev/null")
    run_cmd("make install prefix=test/data/install > /dev/null")
    run_cmd("PYTHONPATH=test/data/install python -c 'import argweaver'")
    assert os.path.exists("test/data/install/bin/arg-sample")
Example #10
0
    def test3(self):
        outdir = 'test/tmp/test_vistrans/Vis_test3/'
        make_clean_dir(outdir)

        stree = treelib.parse_newick(stree_newick)
        tree = treelib.read_tree(treefile3)
        brecon = phylo.read_brecon(breconfile3, tree, stree)

        phylo.add_implied_spec_nodes_brecon(tree, brecon)
        phylo.write_brecon(open(outdir + 'brecon', 'w'), brecon)

        transsvg.draw_tree(tree, brecon, stree, filename=outdir + "tree.svg")
    def test3(self):
        outdir = 'test/tmp/test_vistrans/Vis_test3/'
        make_clean_dir(outdir)

        stree = treelib.parse_newick(stree_newick)
        tree = treelib.read_tree(treefile3)
        brecon = phylo.read_brecon(breconfile3, tree, stree)

        phylo.add_implied_spec_nodes_brecon(tree, brecon)
        phylo.write_brecon(open(outdir + 'brecon', 'w'), brecon)

        transsvg.draw_tree(tree, brecon, stree, filename=outdir + "tree.svg")
Example #12
0
def test_install_prog():
    """
    Test installing ARGweaver program.

    Use Makefile to install.
    """

    make_clean_dir("test/tmp/install")
    run_cmd("python setup.py clean > /dev/null")
    run_cmd("make install prefix=test/tmp/install > /dev/null")
    run_cmd("PYTHONPATH=test/tmp/install python -c 'import argweaver; "
            "assert argweaver.argweaverc.argweaverclib'")
    assert os.path.exists("test/tmp/install/bin/arg-sample")
Example #13
0
def test_trans_switch():
    """
    Calculate transition probabilities for switch matrix

    Only calculate a single matrix
    """
    create_data = False
    if create_data:
        make_clean_dir('test/data/test_trans_switch')

    # model parameters
    k = 12
    n = 1e4
    rho = 1.5e-8 * 20
    length = 1000
    times = argweaver.get_time_points(ntimes=20, maxtime=200000)
    popsizes = [n] * len(times)
    ntests = 100

    # generate test data
    if create_data:
        for i in range(ntests):
            # Sample ARG with at least one recombination.
            while True:
                arg = argweaver.sample_arg_dsmc(k,
                                                2 * n,
                                                rho,
                                                start=0,
                                                end=length,
                                                times=times)
                if any(x.event == "recomb" for x in arg):
                    break
            arg.write('test/data/test_trans_switch/%d.arg' % i)

    for i in range(ntests):
        print('arg', i)
        arg = arglib.read_arg('test/data/test_trans_switch/%d.arg' % i)
        argweaver.discretize_arg(arg, times)
        recombs = [x.pos for x in arg if x.event == "recomb"]
        pos = recombs[0]
        tree = arg.get_marginal_tree(pos - .5)
        rpos, r, c = next(arglib.iter_arg_sprs(arg, start=pos - .5))
        spr = (r, c)

        if not argweaverc.assert_transition_switch_probs(
                tree, spr, times, popsizes, rho):
            tree2 = tree.get_tree()
            treelib.remove_single_children(tree2)
            treelib.draw_tree_names(tree2, maxlen=5, minlen=5)
            assert False
Example #14
0
def test_read_sites():
    """
    Test reading site files.
    """

    make_clean_dir("test/tmp/test_read_sites")
    os.system("""bin/arg-sim \
        -k 10 -L 10000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3  \
        -o test/tmp/test_read_sites/0 > /dev/null""")

    sites = argweaverc.argweaver_read_sites('test/tmp/test_read_sites/0.sites',
                                            -1, -1)
    argweaverc.argweaver_delete_sites(sites)
Example #15
0
def test_read_sites():
    """
    Test reading site files.
    """

    make_clean_dir("test/tmp/test_read_sites")
    os.system("""bin/arg-sim \
        -k 10 -L 10000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3  \
        -o test/tmp/test_read_sites/0 > /dev/null""")

    sites = argweaverc.argweaver_read_sites(
        'test/tmp/test_read_sites/0.sites', -1, -1)
    argweaverc.argweaver_delete_sites(sites)
Example #16
0
def test_trans_switch():
    """
    Calculate transition probabilities for switch matrix

    Only calculate a single matrix
    """
    create_data = False
    if create_data:
        make_clean_dir('test/data/test_trans_switch')

    # model parameters
    k = 12
    n = 1e4
    rho = 1.5e-8 * 20
    length = 1000
    times = argweaver.get_time_points(ntimes=20, maxtime=200000)
    popsizes = [n] * len(times)
    ntests = 100

    # generate test data
    if create_data:
        for i in range(ntests):
            # Sample ARG with at least one recombination.
            while True:
                arg = argweaver.sample_arg_dsmc(
                    k, 2*n, rho, start=0, end=length, times=times)
                if any(x.event == "recomb" for x in arg):
                    break
            arg.write('test/data/test_trans_switch/%d.arg' % i)

    for i in range(ntests):
        print 'arg', i
        arg = arglib.read_arg('test/data/test_trans_switch/%d.arg' % i)
        argweaver.discretize_arg(arg, times)
        recombs = [x.pos for x in arg if x.event == "recomb"]
        pos = recombs[0]
        tree = arg.get_marginal_tree(pos-.5)
        rpos, r, c = arglib.iter_arg_sprs(arg, start=pos-.5).next()
        spr = (r, c)

        if not argweaverc.assert_transition_switch_probs(
                tree, spr, times, popsizes, rho):
            tree2 = tree.get_tree()
            treelib.remove_single_children(tree2)
            treelib.draw_tree_names(tree2, maxlen=5, minlen=5)
            assert False
Example #17
0
def test_install_lib():
    """
    Test installing ARGweaver python lib.

    Use setup.py to install and check that module can be imported.
    Also ensure that c library is installed.
    """

    make_clean_dir("test/tmp/install_lib")
    run_cmd("python setup.py clean > /dev/null")
    run_cmd(
        "python setup.py install --prefix=test/tmp/install_lib "
        "--install-lib=test/tmp/install_lib/lib/python/site-packages "
        "> /dev/null")
    run_cmd("cd test; PYTHONPATH=tmp/install_lib/lib/python/site-packages "
            "python -c 'import argweaver; "
            "assert argweaver.argweaverc.argweaverclib'")
Example #18
0
    def test_top(self):

        outdir = 'test/tmp/test_coal/BMC_test_top/'
        make_clean_dir(outdir)

        stree = treelib.parse_newick(
            "(((A:200, E:200):800, B:1000):500, (C:700, D:700):800);")
        n = 500
        T = 2000
        nsamples = 4000

        # compare top hist with simpler rejection sampling
        tops = {}
        tops2 = {}

        for i in xrange(nsamples):
            # use rejection sampling
            tree, recon = coal.sample_bounded_multicoal_tree_reject(
                stree, n, T, namefunc=lambda x: x)

            # sample tree
            tree2, recon2 = coal.sample_bounded_multicoal_tree(
                stree, n, T, namefunc=lambda x: x)

            top = phylo.hash_tree(tree)
            top2 = phylo.hash_tree(tree2)

            tops.setdefault(top, [0, tree, recon])[0] += 1
            tops.setdefault(top2, [0, tree2, recon2])

            tops2.setdefault(top2, [0, tree2, recon2])[0] += 1
            tops2.setdefault(top, [0, tree, recon])

        keys = tops.keys()
        x = [safelog(tops[i][0], default=0) for i in keys]
        y = [safelog(tops2[i][0], default=0) for i in keys]

        self.assertTrue(stats.corr(x, y) > .9)

        p = Gnuplot()
        p.enableOutput(False)
        p.plot(x, y)
        p.plot([min(x), max(x)], [min(x), max(x)], style="lines")
        p.enableOutput(True)
        p.save(outdir + 'plot.png')
Example #19
0
    def test_sample_lineages(self):
        """lineage over time"""

        outdir = 'test/tmp/test_arglib/Arg_test_sample_lineages/'
        make_clean_dir(outdir)

        rho = 1.5e-8  # recomb/site/gen
        l = 5000      # length of locus
        k = 60        # number of lineages
        n = 2*10000   # effective popsize
        r = rho * l   # recomb/locus/gen

        rplot_start(outdir + '/plot.pdf')
        rp.plot([1, 40000], [1, k],  t="n", log="xy")
        times, events = arglib.sample_coal_recomb_times(k, n, r)
        lineages = list(arglib.lineages_over_time(k, events))
        rp.lines(times, lineages)
        rplot_end()
Example #20
0
def test_install_sdist():
    """
    Test installing ARGweaver from a sdist.
    """

    make_clean_dir("test/tmp/install_sdist")
    run_cmd("python setup.py clean > /dev/null")
    run_cmd("python setup.py sdist --dist-dir=test/tmp/install_sdist")
    run_cmd("cd test/tmp/install_sdist; "
        "tar zxvf *.tar.gz; "
        "cd argweaver-*; "
        "python setup.py install --prefix=. "
        "--install-lib=lib/python/site-packages "
        "> /dev/null")
    run_cmd("cd test/tmp/install_sdist/argweaver-*; "
            "PYTHONPATH=lib/python/site-packages "
            "python -c 'import argweaver; "
            "assert argweaver.argweaverc.argweaverclib'")
Example #21
0
def _test_prog_infsites():

    make_clean_dir("test/data/test_prog_infsites")

    run_cmd("""bin/arg-sim \
        -k 40 -L 200000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 --infsites \
        --ntimes 20 --maxtime 400e3 \
        -o test/data/test_prog_infsites/0""")

    make_clean_dir("test/data/test_prog_infsites/0.sample")
    run_cmd("""bin/arg-sample \
        -s test/data/test_prog_infsites/0.sites \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 5 --maxtime 100e3 -c 1 \
        --climb 0 -n 20 --infsites \
        -x 1 \
        -o test/data/test_prog_infsites/0.sample/out""")

    arg = argweaver.read_arg(
        "test/data/test_prog_infsites/0.sample/out.0.smc.gz")
    sites = argweaver.read_sites("test/data/test_prog_infsites/0.sites")
    print "names", sites.names
    print

    noncompats = []
    for block, tree in arglib.iter_local_trees(arg):
        tree = tree.get_tree()
        treelib.remove_single_children(tree)
        phylo.hash_order_tree(tree)
        for pos, col in sites.iter_region(block[0]+1, block[1]+1):
            assert block[0]+1 <= pos <= block[1]+1, (block, pos)
            split = sites_split(sites.names, col)
            node = arglib.split_to_tree_branch(tree, split)
            if node is None:
                noncompats.append(pos)
                print "noncompat", block, pos, col
                print phylo.hash_tree(tree)
                print tree.leaf_names()
                print "".join(col[sites.names.index(name)]
                              for name in tree.leaf_names())
                print split
                print
    print "num noncompats", len(noncompats)
Example #22
0
def _test_prog_infsites():

    make_clean_dir("test/tmp/test_prog_infsites")

    run_cmd("""bin/arg-sim \
        -k 40 -L 200000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 --infsites \
        --ntimes 20 --maxtime 400e3 \
        -o test/tmp/test_prog_infsites/0""")

    make_clean_dir("test/tmp/test_prog_infsites/0.sample")
    run_cmd("""bin/arg-sample \
        -s test/tmp/test_prog_infsites/0.sites \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 5 --maxtime 100e3 -c 1 \
        --climb 0 -n 20 --infsites \
        -x 1 \
        -o test/tmp/test_prog_infsites/0.sample/out""")

    arg = argweaver.read_arg(
        "test/tmp/test_prog_infsites/0.sample/out.0.smc.gz")
    sites = argweaver.read_sites("test/tmp/test_prog_infsites/0.sites")
    print "names", sites.names
    print

    noncompats = []
    for block, tree in arglib.iter_local_trees(arg):
        tree = tree.get_tree()
        treelib.remove_single_children(tree)
        phylo.hash_order_tree(tree)
        for pos, col in sites.iter_region(block[0] + 1, block[1] + 1):
            assert block[0] + 1 <= pos <= block[1] + 1, (block, pos)
            split = sites_split(sites.names, col)
            node = arglib.split_to_tree_branch(tree, split)
            if node is None:
                noncompats.append(pos)
                print "noncompat", block, pos, col
                print phylo.hash_tree(tree)
                print tree.leaf_names()
                print "".join(col[sites.names.index(name)]
                              for name in tree.leaf_names())
                print split
                print
    print "num noncompats", len(noncompats)
Example #23
0
def test_prog_small():
    """
    Test arg-sample on a small simulated dataset
    """

    make_clean_dir("test/data/test_prog_small")
    run_cmd("""bin/arg-sim \
        -k 4 -L 100000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3  \
        -o test/data/test_prog_small/0 > /dev/null""")

    make_clean_dir("test/data/test_prog_small/0.sample")
    run_cmd("""bin/arg-sample -q \
        -s test/data/test_prog_small/0.sites \
        -x 1 -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3 -c 20 \
        -n 10 --sample-step 1 \
        -o test/data/test_prog_small/0.sample/out""")
Example #24
0
    def test_prob_coal2(self):

        outdir = 'test/tmp/test_coal/Coal_test_prob_coal2/'
        make_clean_dir(outdir)

        k = 2
        n = 1000
        p = Gnuplot()
        p.enableOutput(False)
        p.plotfunc(lambda t: coal.prob_coal(t, k, n), 0, 4000, 10,
                   ymin=0)

        # draw single coal samples
        x = [coal.sample_coal(k, n) for i in xrange(200)]
        plotdistrib(x, 40, plot=p)
        p.enableOutput(True)
        p.save(outdir + 'plot.png')

        eq_sample_pdf(x, lambda t: coal.prob_coal(t, k, n), 40)
Example #25
0
def test_prog_small():
    """
    Test arg-sample on a small simulated dataset
    """

    make_clean_dir("test/tmp/test_prog_small")
    run_cmd("""bin/arg-sim \
        -k 4 -L 100000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3  \
        -o test/tmp/test_prog_small/0 > /dev/null""")

    make_clean_dir("test/tmp/test_prog_small/0.sample")
    run_cmd("""bin/arg-sample -q \
        -s test/tmp/test_prog_small/0.sites \
        -x 1 -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3 -c 20 \
        -n 10 --sample-step 1 \
        -o test/tmp/test_prog_small/0.sample/out""")
Example #26
0
def test_prog_popsizes():
    """
    Ensure arg-sample can use multiple population sizes from a file.
    """

    make_clean_dir("test/tmp/test_prog_popsizes")

    # Setup popsize config file.
    popsizes = range(10000, 0, -1000)
    with open('test/tmp/test_prog_popsizes/popsizes', 'w') as out:
        out.write('\n'.join(map(str, popsizes)))

    run_cmd("""bin/arg-sim \
        -k 4 -L 100000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3  \
        -o test/tmp/test_prog_popsizes/0 > /dev/null""")

    make_clean_dir("test/tmp/test_prog_popsizes/0.sample")
    run_cmd("""bin/arg-sample -q \
        -s test/tmp/test_prog_popsizes/0.sites \
        -x 1 -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3 -c 20 \
        --popsize-file test/tmp/test_prog_popsizes/popsizes \
        -n 10 --sample-step 1 \
        -o test/tmp/test_prog_popsizes/0.sample/out""")

    # Write too few population sizes to config file.
    popsizes_bad = range(10000, 5000, -1000)
    with open('test/tmp/test_prog_popsizes/popsizes-bad', 'w') as out:
        out.write('\n'.join(map(str, popsizes_bad)))

    # Expect an error.
    run_cmd(
        """bin/arg-sample -q \
        -s test/tmp/test_prog_popsizes/0.sites \
        -x 1 -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3 -c 20 \
        --popsize-file test/tmp/test_prog_popsizes/popsizes-bad \
        -n 10 --sample-step 1 \
        -o test/tmp/test_prog_popsizes/0.sample/out-bad""", EXIT_ERROR)
Example #27
0
def test_prog_popsizes():
    """
    Ensure arg-sample can use multiple population sizes from a file.
    """

    make_clean_dir("test/tmp/test_prog_popsizes")

    # Setup popsize config file.
    popsizes = range(10000, 0, -1000)
    with open('test/tmp/test_prog_popsizes/popsizes', 'w') as out:
        out.write('\n'.join(map(str, popsizes)))

    run_cmd("""bin/arg-sim \
        -k 4 -L 100000 \
        -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3  \
        -o test/tmp/test_prog_popsizes/0 > /dev/null""")

    make_clean_dir("test/tmp/test_prog_popsizes/0.sample")
    run_cmd("""bin/arg-sample -q \
        -s test/tmp/test_prog_popsizes/0.sites \
        -x 1 -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3 -c 20 \
        --popsize-file test/tmp/test_prog_popsizes/popsizes \
        -n 10 --sample-step 1 \
        -o test/tmp/test_prog_popsizes/0.sample/out""")

    # Write too few population sizes to config file.
    popsizes_bad = range(10000, 5000, -1000)
    with open('test/tmp/test_prog_popsizes/popsizes-bad', 'w') as out:
        out.write('\n'.join(map(str, popsizes_bad)))

    # Expect an error.
    run_cmd("""bin/arg-sample -q \
        -s test/tmp/test_prog_popsizes/0.sites \
        -x 1 -N 1e4 -r 1.5e-8 -m 2.5e-8 \
        --ntimes 10 --maxtime 400e3 -c 20 \
        --popsize-file test/tmp/test_prog_popsizes/popsizes-bad \
        -n 10 --sample-step 1 \
        -o test/tmp/test_prog_popsizes/0.sample/out-bad""",
            EXIT_ERROR)
Example #28
0
    def test_cdf_mrca(self):

        outdir = 'test/tmp/test_coal/Coal_test_cdf_mrca/'
        make_clean_dir(outdir)

        n = 1000
        k = 6
        step = 10
        x = list(frange(0, 5000, step))
        y = [coal.prob_mrca(i, k, n) * step for i in x]
        y2 = cumsum(y)
        y3 = [coal.cdf_mrca(t, k, n) for t in x]

        p = Gnuplot()
        p.enableOutput(False)
        p.plot(x, y2, style="lines")
        p.plot(x, y3, style="lines")
        p.enableOutput(True)
        p.save(outdir + 'plot.png')

        eq_sample_pdf(x, lambda t: coal.cdf_mrca(t, k, n), 40)
Example #29
0
    def test_prob_coal_cond_counts_simple(self):

        # when we condition on b=1, it is the same as the bounded coal
        # PDF.
        # prob_coal_cond_counts is actually a more general version of
        # prob_bounded_coal

        outdir = 'test/tmp/test_coal/Coal_test_prob_coal_counys_simple/'
        make_clean_dir(outdir)

        a = 5
        b = 1
        t = 2000
        n = 1000
        p = Gnuplot()
        p.enableOutput(False)

        for x in frange(0, 2000, 10):
            y = coal.prob_coal_cond_counts_simple(x, a, b, t, n)
            y2 = coal.prob_bounded_coal(x, a, n, t)
            self.assertAlmostEqual(y, y2)
Example #30
0
    def test_coin(self):
        """Test that viterbi and posterior coding work well."""

        outdir = 'test/tmp/test_hmm/test_coin/'
        make_clean_dir(outdir)

        model = make_coin_model()

        # sample states
        ndata = 100
        states = list(islice(hmm.sample_hmm_states(model), ndata))
        p = Gnuplot()
        p.enableOutput(False)
        p.plot(states, style="lines")

        # sample data
        data = list(hmm.sample_hmm_data(model, states))

        # viterbi
        model.prob_emission = (
            lambda pos, state: model.prob_emission_data(state, data[pos]))
        states2 = hmm.viterbi(model, len(data))

        # posterior
        probs = hmm.get_posterior_probs(model, len(data))
        states3 = [exp(probs[i][1]) for i in xrange(len(data))]

        # assert that inferences correlates with true state
        self.assertTrue(stats.corr(states, states2) > .5)
        self.assertTrue(stats.corr(states, states3) > .5)

        # plot inference
        p.plot(util.vadds(states2, 1.5), style="lines", miny=-1, maxy=4)
        p.plot(util.vadds(states3, 2.5), style="lines", miny=-1, maxy=4)
        p.enableOutput(True)
        p.save(outdir + 'plot.png')
    def test_coin(self):
        """Test that viterbi and posterior coding work well."""

        outdir = 'test/tmp/test_hmm/test_coin/'
        make_clean_dir(outdir)

        model = make_coin_model()

        # sample states
        ndata = 100
        states = list(islice(hmm.sample_hmm_states(model), ndata))
        p = Gnuplot()
        p.enableOutput(False)
        p.plot(states, style="lines")

        # sample data
        data = list(hmm.sample_hmm_data(model, states))

        # viterbi
        model.prob_emission = (lambda pos, state:
                               model.prob_emission_data(state, data[pos]))
        states2 = hmm.viterbi(model, len(data))

        # posterior
        probs = hmm.get_posterior_probs(model, len(data))
        states3 = [exp(probs[i][1]) for i in xrange(len(data))]

        # assert that inferences correlates with true state
        self.assertTrue(stats.corr(states, states2) > .5)
        self.assertTrue(stats.corr(states, states3) > .5)

        # plot inference
        p.plot(util.vadds(states2, 1.5), style="lines", miny=-1, maxy=4)
        p.plot(util.vadds(states3, 2.5), style="lines", miny=-1, maxy=4)
        p.enableOutput(True)
        p.save(outdir + 'plot.png')