コード例 #1
0
ファイル: test_basic.py プロジェクト: swamidass/argweaver
    def test_backward_c(self):

        k = 3
        n = 1e4
        rho = 1.5e-8 * 30
        mu = 2.5e-8 * 100
        length = 100
        arg = arglib.sample_arg(k, n, rho, start=0, end=length)
        arg.prune()
        muts = arglib.sample_arg_mutations(arg, mu)
        seqs = arglib.make_alignment(arg, muts)

        print arglib.get_recomb_pos(arg)
        print "muts", len(muts)
        print "recomb", len(arglib.get_recomb_pos(arg))

        times = arghmm.get_time_points(ntimes=10)
        arghmm.discretize_arg(arg, times)

        tree = arg.get_marginal_tree(0)
        print tree.root.age
        treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)

        # remove chrom
        keep = ["n%d" % i for i in range(k - 1)]
        arglib.subarg_by_leaf_names(arg, keep)

        model = arghmm.ArgHmm(arg,
                              seqs,
                              new_name="n%d" % (k - 1),
                              times=times,
                              rho=rho,
                              mu=mu)
        print "states", len(model.states[0])

        util.tic("C")
        probs1 = list(arghmm.backward_algorithm(model, length, verbose=True))
        util.toc()

        util.tic("python")
        probs2 = list(hmm.backward_algorithm(model, length, verbose=True))
        util.toc()

        print "probs1"
        pc(probs1)

        print "probs2"
        pc(probs2)

        for col1, col2 in izip(probs1, probs2):
            for a, b in izip(col1, col2):
                fequal(a, b)
コード例 #2
0
ファイル: test_basic.py プロジェクト: bredelings/argweaver
    def test_backward_c(self):

        k = 3
        n = 1e4
        rho = 1.5e-8 * 30
        mu = 2.5e-8 * 100
        length = 100
        arg = arglib.sample_arg(k, n, rho, start=0, end=length)
        arg.prune()
        muts = arglib.sample_arg_mutations(arg, mu)
        seqs = arglib.make_alignment(arg, muts)

        print arglib.get_recomb_pos(arg)
        print "muts", len(muts)
        print "recomb", len(arglib.get_recomb_pos(arg))

        times = arghmm.get_time_points(ntimes=10)
        arghmm.discretize_arg(arg, times)

        tree = arg.get_marginal_tree(0)
        print tree.root.age
        treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)

        # remove chrom
        keep = ["n%d" % i for i in range(k-1)]
        arglib.subarg_by_leaf_names(arg, keep)

        model = arghmm.ArgHmm(arg, seqs, new_name="n%d" % (k-1), times=times,
                              rho=rho, mu=mu)
        print "states", len(model.states[0])

        util.tic("C")
        probs1 = list(arghmm.backward_algorithm(model, length, verbose=True))
        util.toc()

        util.tic("python")
        probs2 = list(hmm.backward_algorithm(model, length, verbose=True))
        util.toc()

        print "probs1"
        pc(probs1)

        print "probs2"
        pc(probs2)


        for col1, col2 in izip(probs1, probs2):
            for a, b in izip(col1, col2):
                fequal(a, b)
コード例 #3
0
ファイル: test_basic.py プロジェクト: swamidass/argweaver
    def test_backward(self):
        """
        Run backward algorithm
        """

        k = 3
        n = 1e4
        rho = 1.5e-8 * 100
        mu = 2.5e-8 * 100
        length = 10000
        arg = arglib.sample_arg(k, n, rho, start=0, end=length)
        muts = arglib.sample_arg_mutations(arg, mu)
        seqs = arglib.make_alignment(arg, muts)

        times = arghmm.get_time_points(ntimes=10)
        arghmm.discretize_arg(arg, times)

        tree = arg.get_marginal_tree(0)
        print tree.root.age
        treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)

        # remove chrom
        new_name = "n%d" % (k - 1)
        arg = arghmm.remove_arg_thread(arg, new_name)

        model = arghmm.ArgHmm(arg,
                              seqs,
                              new_name=new_name,
                              times=times,
                              rho=rho,
                              mu=mu)
        print "states", len(model.states[0])
        print "recomb", model.recomb_pos
        print "muts", len(muts)

        probs = hmm.backward_algorithm(model, length, verbose=True)

        for pcol in probs:
            p = sum(map(exp, pcol))
            print p, " ".join("%.3f" % f for f in map(exp, pcol))
コード例 #4
0
ファイル: test_basic.py プロジェクト: bredelings/argweaver
    def test_backward(self):
        """
        Run backward algorithm
        """

        k = 3
        n = 1e4
        rho = 1.5e-8 * 100
        mu = 2.5e-8 * 100
        length = 10000
        arg = arglib.sample_arg(k, n, rho, start=0, end=length)
        muts = arglib.sample_arg_mutations(arg, mu)
        seqs = arglib.make_alignment(arg, muts)

        times = arghmm.get_time_points(ntimes=10)
        arghmm.discretize_arg(arg, times)

        tree = arg.get_marginal_tree(0)
        print tree.root.age
        treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)

        # remove chrom
        new_name = "n%d" % (k-1)
        arg = arghmm.remove_arg_thread(arg, new_name)

        model = arghmm.ArgHmm(arg, seqs, new_name=new_name, times=times,
                              rho=rho, mu=mu)
        print "states", len(model.states[0])
        print "recomb", model.recomb_pos
        print "muts", len(muts)

        probs = hmm.backward_algorithm(model, length, verbose=True)

        for pcol in probs:
            p = sum(map(exp, pcol))
            print p, " ".join("%.3f" % f for f in map(exp, pcol))