Пример #1
0
def get_response_content(fs):
    flags = get_flags(fs)
    nseconds = 5
    tm = time.time()
    rejected_s = None
    nerrors = 0
    nchecked = 0
    while time.time() < tm + nseconds and not rejected_s:
        nchecked += 1
        # Sample a Newick tree.
        true_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
        true_s = NewickIO.get_newick_string(true_f)
        true_tree = Newick.parse(true_s, Newick.NewickTree)
        # Get the leaf and internal vertex ids for the true tree.
        internal_ids = set(id(x) for x in true_tree.gen_internal_nodes())
        leaf_ids = set(id(x) for x in true_tree.gen_tips())
        nleaves = len(leaf_ids)
        # Get the harmonic valuations for all vertices of the tree.
        id_to_full_val_list = [
            Harmonic.get_harmonic_valuations(true_tree, i)
            for i in range(1, nleaves)
        ]
        # Check for small valuations at the leaves.
        try:
            for id_to_full_val in id_to_full_val_list:
                for x in leaf_ids:
                    value = id_to_full_val[x]
                    if abs(value) < 1e-8:
                        raise CheckTreeError('the true tree is too symmetric')
        except CheckTreeError as e:
            nerrors += 1
            continue
        # Assign the leaf values and assign None to internal values.
        id_to_val_list = []
        for id_to_full_val in id_to_full_val_list:
            d = {}
            for x in leaf_ids:
                s = -1 if id_to_full_val[x] < 0 else 1
                d[x] = s
            for x in internal_ids:
                d[x] = None
            id_to_val_list.append(d)
        # Define the topology in a different format.
        id_to_adj = get_id_to_adj(true_tree)
        # Check the tree for self-compatibility under the given conditions.
        id_to_vals = SeekEigenLacing.rec_eigen(id_to_adj, id_to_val_list,
                                               flags)
        if not id_to_vals:
            rejected_s = true_s
    # make the report
    out = StringIO()
    if rejected_s:
        print >> out, 'rejected a true tree:'
        print >> out, rejected_s
    else:
        print >> out, 'no true tree was rejected'
    print >> out
    print >> out, nchecked, 'trees were sampled total'
    print >> out, nerrors, 'trees were too symmetric'
    return out.getvalue()
Пример #2
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def gen_trees():
    n_base_leaves = 4
    n_expected_extra_leaves = 1
    expected_branch_length = 1
    while True:
        yield TreeSampler.sample_tree(n_base_leaves, n_expected_extra_leaves,
                                      expected_branch_length)
Пример #3
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def gen_trees():
    n_base_leaves = 4
    n_expected_extra_leaves = 1
    expected_branch_length = 1
    while True:
        yield TreeSampler.sample_tree(
                n_base_leaves, n_expected_extra_leaves, expected_branch_length)
Пример #4
0
def get_response_content(fs):
    flags = get_flags(fs)
    nseconds = 5
    tm = time.time()
    rejected_s = None
    nerrors = 0
    nchecked = 0
    while time.time() < tm + nseconds and not rejected_s:
        nchecked += 1
        # Sample a Newick tree.
        true_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
        true_s = NewickIO.get_newick_string(true_f)
        true_tree = Newick.parse(true_s, Newick.NewickTree)
        # Get the leaf and internal vertex ids for the true tree.
        internal_ids = set(id(x) for x in true_tree.gen_internal_nodes())
        leaf_ids = set(id(x) for x in true_tree.gen_tips())
        nleaves = len(leaf_ids)
        # Get the harmonic valuations for all vertices of the tree.
        id_to_full_val_list = [Harmonic.get_harmonic_valuations(
            true_tree, i) for i in range(1, nleaves)]
        # Check for small valuations at the leaves.
        try:
            for id_to_full_val in id_to_full_val_list:
                for x in leaf_ids:
                    value = id_to_full_val[x]
                    if abs(value) < 1e-8:
                        raise CheckTreeError('the true tree is too symmetric')
        except CheckTreeError as e:
            nerrors += 1
            continue
        # Assign the leaf values and assign None to internal values.
        id_to_val_list = []
        for id_to_full_val in id_to_full_val_list:
            d = {}
            for x in leaf_ids:
                s = -1 if id_to_full_val[x] < 0 else 1
                d[x] = s
            for x in internal_ids:
                d[x] = None
            id_to_val_list.append(d)
        # Define the topology in a different format.
        id_to_adj = get_id_to_adj(true_tree)
        # Check the tree for self-compatibility under the given conditions.
        id_to_vals = SeekEigenLacing.rec_eigen(
                id_to_adj, id_to_val_list, flags)
        if not id_to_vals:
            rejected_s = true_s
    # make the report
    out = StringIO()
    if rejected_s:
        print >> out, 'rejected a true tree:'
        print >> out, rejected_s
    else:
        print >> out, 'no true tree was rejected'
    print >> out
    print >> out, nchecked, 'trees were sampled total'
    print >> out, nerrors, 'trees were too symmetric'
    return out.getvalue()
Пример #5
0
def main():
    filename = 'counterexamples.out'
    fout = open(filename, 'wt')
    print 'Does monotonically transforming the pairwise leaf distances affect the compatibility'
    print 'of the split found using principal coordinate analysis?'
    print 'I am looking through random trees for a tree that is split incompatibly'
    print 'when distances are squared.'
    print 'Use control-c to stop the program when you get bored.'
    try:
        count = 0
        ncounterexamples = 0
        nerrors = 0
        while True:
            count += 1
            # get a random tree
            n_base_leaves = 4
            n_expected_extra_leaves = 1
            expected_branch_length = 1
            tree = TreeSampler.sample_tree(n_base_leaves,
                                           n_expected_extra_leaves,
                                           expected_branch_length)
            # get the set of valid partitions implied by the tree
            valid_parts = TreeComparison.get_partitions(tree)
            ordered_tip_names = [tip.get_name() for tip in tree.gen_tips()]
            # assert that the partition implied by the correct formula is valid
            D = np.array(tree.get_distance_matrix(ordered_tip_names))
            loadings = get_principal_coordinate(D)
            nonneg_leaf_set = frozenset(
                tip for tip, v in zip(ordered_tip_names, loadings) if v >= 0)
            neg_leaf_set = frozenset(
                tip for tip, v in zip(ordered_tip_names, loadings) if v < 0)
            part = frozenset([nonneg_leaf_set, neg_leaf_set])
            if part not in valid_parts:
                nerrors += 1
                print >> fout, 'error: a partition that was supposed to be valid was found to be invalid'
                print >> fout, 'tree:', NewickIO.get_newick_string(tree)
                print >> fout, 'invalid partition:', partition_to_string(part)
                print >> fout
            # check the validity of the partition implied by the incorrect formula
            Q = D * D
            loadings = get_principal_coordinate(Q)
            nonneg_leaf_set = frozenset(
                tip for tip, v in zip(ordered_tip_names, loadings) if v >= 0)
            neg_leaf_set = frozenset(
                tip for tip, v in zip(ordered_tip_names, loadings) if v < 0)
            part = frozenset([nonneg_leaf_set, neg_leaf_set])
            if part not in valid_parts:
                ncounterexamples += 1
                print >> fout, 'found a counterexample!'
                print >> fout, 'tree:', NewickIO.get_newick_string(tree)
                print >> fout, 'invalid partition:', partition_to_string(part)
                print >> fout
    except KeyboardInterrupt, e:
        print 'trees examined:', count
        print 'errors:', nerrors
        print 'counterexamples:', ncounterexamples
Пример #6
0
def get_response_content(fs):
    flags_a = get_flags_a(fs)
    flags_b = get_flags_b(fs)
    data = CheckTreeData(flags_a, flags_b)
    nseconds = 5
    tm = time.time()
    while time.time() < tm + nseconds:
        # Sample a pair of Newick trees.
        true_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
        test_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
        true_s = NewickIO.get_newick_string(true_f)
        test_s = NewickIO.get_newick_string(test_f)
        true_tree = Newick.parse(true_s, Newick.NewickTree)
        test_tree = Newick.parse(test_s, Newick.NewickTree)
        # Add the pairwise check to the data borg.
        try:
            found_difference = check_tree_pair(true_tree, test_tree, data)
        except CheckTreeError as e:
            data.add_error(e)
        # Check to see if we should stop early.
        if found_difference and fs.halt_on_difference:
            break
    # make the report
    out = StringIO()
    if data.report:
        print >> out, 'found a difference in rejection power'
        print >> out
        print >> out, data.report
        print >> out
    else:
        print >> out, 'failed to find a difference in rejection power'
        print >> out
    print >> out, 'search summary:'
    m = data.acceptance_matrix
    print >> out, 'A reject, B reject:', m[0, 0]
    print >> out, 'A reject, B accept:', m[0, 1]
    print >> out, 'A accept, B reject:', m[1, 0]
    print >> out, 'A accept, B accept:', m[1, 1]
    print >> out, data.nerrors, 'tree symmetry errors'
    return out.getvalue()
Пример #7
0
def get_response_content(fs):
    flags_a = get_flags_a(fs)
    flags_b = get_flags_b(fs)
    data = CheckTreeData(flags_a, flags_b)
    nseconds = 5
    tm = time.time()
    while time.time() < tm + nseconds:
        # Sample a pair of Newick trees.
        true_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
        test_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
        true_s = NewickIO.get_newick_string(true_f)
        test_s = NewickIO.get_newick_string(test_f)
        true_tree = Newick.parse(true_s, Newick.NewickTree)
        test_tree = Newick.parse(test_s, Newick.NewickTree)
        # Add the pairwise check to the data borg.
        try:
            found_difference = check_tree_pair(true_tree, test_tree, data)
        except CheckTreeError as e:
            data.add_error(e)
        # Check to see if we should stop early.
        if found_difference and fs.halt_on_difference:
            break
    # make the report
    out = StringIO()
    if data.report:
        print >> out, 'found a difference in rejection power'
        print >> out
        print >> out, data.report
        print >> out
    else:
        print >> out, 'failed to find a difference in rejection power'
        print >> out
    print >> out, 'search summary:'
    m = data.acceptance_matrix
    print >> out, 'A reject, B reject:', m[0, 0]
    print >> out, 'A reject, B accept:', m[0, 1]
    print >> out, 'A accept, B reject:', m[1, 0]
    print >> out, 'A accept, B accept:', m[1, 1]
    print >> out, data.nerrors, 'tree symmetry errors'
    return out.getvalue()
Пример #8
0
def get_response_content(fs):
    """
    @param fs: a FieldStorage object containing the cgi arguments
    @return: a (response_headers, response_text) pair
    """
    out = StringIO()
    # get some samples
    for i in range(fs.ntrees):
        tree = TreeSampler.sample_tree(fs.leafbase, fs.leafmean, fs.branchmean)
        # write the tree
        print >> out, NewickIO.get_newick_string(tree)
    # return the response
    return out.getvalue()
Пример #9
0
def get_response_content(fs):
    """
    @param fs: a FieldStorage object containing the cgi arguments
    @return: a (response_headers, response_text) pair
    """
    out = StringIO()
    # get some samples
    for i in range(fs.ntrees):
        tree = TreeSampler.sample_tree(fs.leafbase, fs.leafmean, fs.branchmean)
        # write the tree
        print >> out, NewickIO.get_newick_string(tree)
    # return the response
    return out.getvalue()
Пример #10
0
def main():
    filename = 'counterexamples.out'
    fout = open(filename, 'wt')
    print 'Does monotonically transforming the pairwise leaf distances affect the compatibility'
    print 'of the split found using principal coordinate analysis?'
    print 'I am looking through random trees for a tree that is split incompatibly'
    print 'when distances are squared.'
    print 'Use control-c to stop the program when you get bored.'
    try:
        count = 0
        ncounterexamples = 0
        nerrors = 0
        while True:
            count += 1
            # get a random tree
            n_base_leaves = 4
            n_expected_extra_leaves = 1
            expected_branch_length = 1
            tree = TreeSampler.sample_tree(n_base_leaves, n_expected_extra_leaves, expected_branch_length)
            # get the set of valid partitions implied by the tree
            valid_parts = TreeComparison.get_partitions(tree)
            ordered_tip_names = [tip.get_name() for tip in tree.gen_tips()]
            # assert that the partition implied by the correct formula is valid
            D = np.array(tree.get_distance_matrix(ordered_tip_names))
            loadings = get_principal_coordinate(D)
            nonneg_leaf_set = frozenset(tip for tip, v in zip(ordered_tip_names, loadings) if v >= 0)
            neg_leaf_set = frozenset(tip for tip, v in zip(ordered_tip_names, loadings) if v < 0)
            part = frozenset([nonneg_leaf_set, neg_leaf_set])
            if part not in valid_parts:
                nerrors += 1
                print >> fout, 'error: a partition that was supposed to be valid was found to be invalid'
                print >> fout, 'tree:', NewickIO.get_newick_string(tree)
                print >> fout, 'invalid partition:', partition_to_string(part)
                print >> fout
            # check the validity of the partition implied by the incorrect formula
            Q = D * D
            loadings = get_principal_coordinate(Q)
            nonneg_leaf_set = frozenset(tip for tip, v in zip(ordered_tip_names, loadings) if v >= 0)
            neg_leaf_set = frozenset(tip for tip, v in zip(ordered_tip_names, loadings) if v < 0)
            part = frozenset([nonneg_leaf_set, neg_leaf_set])
            if part not in valid_parts:
                ncounterexamples += 1
                print >> fout, 'found a counterexample!'
                print >> fout, 'tree:', NewickIO.get_newick_string(tree)
                print >> fout, 'invalid partition:', partition_to_string(part)
                print >> fout
    except KeyboardInterrupt, e:
        print 'trees examined:', count
        print 'errors:', nerrors
        print 'counterexamples:', ncounterexamples