Example #1
0
    def test_read_write(self):
        """Read and write an ARG"""

        rho = 1.5e-8   # recomb/site/gen
        l = 10000      # length of locus
        k = 10         # number of lineages
        n = 2*10000    # effective popsize

        arg = arglib.sample_arg(k, n, rho, 0, l)
        # round ages and pos for easy equality
        for node in arg:
            node.age = round(node.age)
            node.pos = round(node.pos)

        stream = StringIO.StringIO()
        arglib.write_arg(stream, arg)
        stream.seek(0)
        arg2 = arglib.read_arg(stream)

        self.assertTrue(arg.equal(arg2))
Example #2
0
    def test_recomb(self):
        """
        Investigate the fact that some recombinations are not visible
        """

        k = 3
        n = 1e4
        rho = 1.5e-8 * 20
        mu = 2.5e-8
        length = 1000
        arg = arglib.sample_arg(k, n, rho, start=0, end=length)

        times = arghmm.get_time_points(10)
        arghmm.discretize_arg(arg, times)
        arg.set_ancestral()
        arg.prune()

        recombs = arglib.get_recomb_pos(arg)

        # find recombs by walking
        recombs2 = []
        i = 0
        while True:
            tree = arg.get_marginal_tree(i - .5)
            recomb = arghmm.find_tree_next_recomb(tree, i + 1, tree=True)
            if recomb:
                recombs2.append(recomb.pos)
                i = recomb.pos
            else:
                break

        # these are suppose to differ because some recombination occur
        # in the hole of ancestral sequence intervals
        print recombs
        print recombs2

        arglib.write_arg("tmp/b.arg", arg)
Example #3
0
    def test_recomb(self):
        """
        Investigate the fact that some recombinations are not visible
        """

        k = 3
        n = 1e4
        rho = 1.5e-8 * 20
        mu = 2.5e-8
        length = 1000
        arg = arglib.sample_arg(k, n, rho, start=0, end=length)

        times = arghmm.get_time_points(10)
        arghmm.discretize_arg(arg, times)
        arg.set_ancestral()
        arg.prune()

        recombs = arglib.get_recomb_pos(arg)

        # find recombs by walking
        recombs2 = []
        i = 0
        while True:
            tree = arg.get_marginal_tree(i-.5)
            recomb = arghmm.find_tree_next_recomb(tree, i+1, tree=True)
            if recomb:
                recombs2.append(recomb.pos)
                i = recomb.pos
            else:
                break

        # these are suppose to differ because some recombination occur
        # in the hole of ancestral sequence intervals
        print recombs
        print recombs2

        arglib.write_arg("tmp/b.arg", arg)
Example #4
0
        move_layout(layout1, x=i*(nleaves+2))
        move_layout(layout2, x=(i+1)*(nleaves+2))
        mapping = get_mapping(tree1, tree2, pos, times)
        draw_mapping(tree1, tree2, layout1, layout2, times, mapping)
        

#=============================================================================
if 0:
    k = 10
    n = 1e4
    rho = 1.5e-8 * 100
    mu = 2.5e-8
    length = 1000
    
    arg = arglib.sample_arg(k, n, rho, start=0, end=length)
    arglib.write_arg("tmp/a.arg", arg)
    muts = arglib.sample_arg_mutations(arg, mu)
    seqs = arglib.make_alignment(arg, muts)

    #arg = arglib.read_arg("tmp/a.arg")
    #arg.set_ancestral()
    #find_recomb_coal(tree, last_tree, recomb_name=None, pos=None)

    times = arghmm.get_time_points(30, maxtime=60e3)
    arghmm.discretize_arg(arg, times)

    # get recombs
    recombs = list(x.pos for x in arghmm.iter_visible_recombs(arg))
    print "recomb", recombs

    pos = recombs[0] + 1
Example #5
0
        #    treelib.layout_tree(tree2, xscale=1, yscale=1), leaves=0)
        move_layout(layout1, x=i * (nleaves + 2))
        move_layout(layout2, x=(i + 1) * (nleaves + 2))
        mapping = get_mapping(tree1, tree2, pos, times)
        draw_mapping(tree1, tree2, layout1, layout2, times, mapping)

#=============================================================================
if 0:
    k = 10
    n = 1e4
    rho = 1.5e-8 * 100
    mu = 2.5e-8
    length = 1000

    arg = arglib.sample_arg(k, n, rho, start=0, end=length)
    arglib.write_arg("tmp/a.arg", arg)
    muts = arglib.sample_arg_mutations(arg, mu)
    seqs = arglib.make_alignment(arg, muts)

    #arg = arglib.read_arg("tmp/a.arg")
    #arg.set_ancestral()
    #find_recomb_coal(tree, last_tree, recomb_name=None, pos=None)

    times = arghmm.get_time_points(30, maxtime=60e3)
    arghmm.discretize_arg(arg, times)

    # get recombs
    recombs = list(x.pos for x in arghmm.iter_visible_recombs(arg))
    print "recomb", recombs

    pos = recombs[0] + 1