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()
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)
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)
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()
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
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()
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()
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()
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()
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
