def __call__(self, tree):
# get the partitions implied by the tree
valid_partitions = TreeComparison.get_partitions(tree)
# Get the partition implied by the Fiedler split
# of the graph derived from the tree.
tip_nodes = list(tree.gen_tips())
D = tree.get_partial_distance_matrix(
[id(node) for node in tip_nodes])
y = get_vector(D).tolist()
name_selection = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y) if elem > 0)
name_complement = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y) if elem <= 0)
name_partition = frozenset((name_selection, name_complement))
if name_partition not in valid_partitions:
msg = '\n'.join([
'invalid partition found:',
'tree:', NewickIO.get_newick_string(tree),
'invalid partition:', name_partition])
if not self.fout:
self.fout = open(self.counterexample_filename, 'wt')
print >> self.fout, msg
print msg
self.ncounterexamples += 1
# do not stop looking, even if a counterexample is found
return False
def __call__(self, tree):
# get the partitions implied by the tree
valid_partitions = TreeComparison.get_partitions(tree)
# Get the partition implied by the Fiedler split
# of the graph derived from the tree.
tip_nodes = list(tree.gen_tips())
D = tree.get_partial_distance_matrix([id(node) for node in tip_nodes])
y = get_vector(D).tolist()
name_selection = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y)
if elem > 0)
name_complement = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y)
if elem <= 0)
name_partition = frozenset((name_selection, name_complement))
if name_partition not in valid_partitions:
msg = '\n'.join([
'invalid partition found:', 'tree:',
NewickIO.get_newick_string(tree), 'invalid partition:',
name_partition
])
if not self.fout:
self.fout = open(self.counterexample_filename, 'wt')
print >> self.fout, msg
print msg
self.ncounterexamples += 1
# do not stop looking, even if a counterexample is found
return False
def get_response_content(fs):
# get the newick trees.
trees = []
for tree_string in iterutils.stripped_lines(StringIO(fs.trees)):
# parse each tree and make sure that it conforms to various requirements
tree = NewickIO.parse(tree_string, FelTree.NewickTree)
tip_names = [tip.get_name() for tip in tree.gen_tips()]
if len(tip_names) < 4:
raise HandlingError('expected at least four tips but found ' +
str(len(tip_names)))
if any(name is None for name in tip_names):
raise HandlingError('each terminal node must be labeled')
if len(set(tip_names)) != len(tip_names):
raise HandlingError('each terminal node label must be unique')
trees.append(tree)
# begin the response
out = StringIO()
# look at each tree
nerrors = 0
ncounterexamples = 0
for tree in trees:
# 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 >> out, 'error: a partition that was supposed to be valid was found to be invalid'
print >> out, 'tree:', NewickIO.get_newick_string(tree)
print >> out, 'invalid partition:', partition_to_string(part)
print >> out
# 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 >> out, 'found a counterexample!'
print >> out, 'tree:', NewickIO.get_newick_string(tree)
print >> out, 'invalid partition:', partition_to_string(part)
print >> out
print >> out, 'errors found:', nerrors
print >> out, 'counterexamples found:', ncounterexamples
# 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
def get_response_content(fs):
# get the newick trees.
trees = []
for tree_string in iterutils.stripped_lines(StringIO(fs.trees)):
# parse each tree and make sure that it conforms to various requirements
tree = NewickIO.parse(tree_string, FelTree.NewickTree)
tip_names = [tip.get_name() for tip in tree.gen_tips()]
if len(tip_names) < 4:
raise HandlingError('expected at least four tips but found ' + str(len(tip_names)))
if any(name is None for name in tip_names):
raise HandlingError('each terminal node must be labeled')
if len(set(tip_names)) != len(tip_names):
raise HandlingError('each terminal node label must be unique')
trees.append(tree)
# begin the response
out = StringIO()
# look at each tree
nerrors = 0
ncounterexamples = 0
for tree in trees:
# 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 >> out, 'error: a partition that was supposed to be valid was found to be invalid'
print >> out, 'tree:', NewickIO.get_newick_string(tree)
print >> out, 'invalid partition:', partition_to_string(part)
print >> out
# 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 >> out, 'found a counterexample!'
print >> out, 'tree:', NewickIO.get_newick_string(tree)
print >> out, 'invalid partition:', partition_to_string(part)
print >> out
print >> out, 'errors found:', nerrors
print >> out, 'counterexamples found:', ncounterexamples
# 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
def get_response_content(fs):
# get the newick trees.
trees = []
for tree_string in iterutils.stripped_lines(fs.trees.splitlines()):
# parse each tree and make sure that it conforms to various requirements
tree = NewickIO.parse(tree_string, FelTree.NewickTree)
tip_names = [tip.get_name() for tip in tree.gen_tips()]
if len(tip_names) < 4:
raise HandlingError('expected at least four tips '
'but found ' + str(len(tip_names)))
if any(name is None for name in tip_names):
raise HandlingError('each terminal node must be labeled')
if len(set(tip_names)) != len(tip_names):
raise HandlingError('each terminal node label must be unique')
trees.append(tree)
# create the response
out = StringIO()
same_count = 0
diff_count = 0
for tree in trees:
# make the local paragraph that will be shown if there is an event
local_out = StringIO()
has_event = False
# print the tree
print >> local_out, NewickIO.get_newick_string(tree)
# get the tip nodes and the internal nodes
tip_nodes = []
internal_nodes = []
for node in tree.preorder():
if node.is_tip():
tip_nodes.append(node)
else:
internal_nodes.append(node)
all_nodes = tip_nodes + internal_nodes
# get all tip name partitions implied by the tree topology
valid_partitions = TreeComparison.get_partitions(tree)
# get results from the augmented distance matrix
D_full = tree.get_partial_distance_matrix(
[id(node) for node in all_nodes])
y_full = get_vector(D_full).tolist()
y = y_full[:len(tip_nodes)]
name_selection = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y)
if elem > 0)
name_complement = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y)
if elem <= 0)
name_partition_a = frozenset((name_selection, name_complement))
if name_partition_a not in valid_partitions:
print >> local_out, 'augmented distance matrix split fail:',
print >> local_out, name_partition_a
has_event = True
# get results from the not-augmented distance matrix
D = tree.get_partial_distance_matrix([id(node) for node in tip_nodes])
y = get_vector(D).tolist()
name_selection = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y)
if elem > 0)
name_complement = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y)
if elem <= 0)
name_partition_b = frozenset((name_selection, name_complement))
if name_partition_b not in valid_partitions:
print >> local_out, 'not-augmented distance matrix split fail:',
print >> local_out, name_partition_b
has_event = True
# compare the name partitions
if name_partition_a == name_partition_b:
same_count += 1
else:
diff_count += 1
print >> local_out, 'this tree was split differently '
print >> local_out, 'by the different methods:'
print >> local_out, 'augmented distance matrix split:',
print >> local_out, name_partition_a
print >> local_out, 'not-augmented distance matrix split:',
print >> local_out, name_partition_b
has_event = True
# print a newline between trees
if has_event:
print >> out, local_out.getvalue()
# write the summary
print >> out, 'for this many trees the same split was found:',
print >> out, same_count
print >> out, 'for this many trees different splits were found:',
print >> out, diff_count
# write the response
return out.getvalue()
def get_response_content(fs):
# get the newick trees.
trees = []
for tree_string in iterutils.stripped_lines(fs.trees.splitlines()):
# parse each tree and make sure that it conforms to various requirements
tree = NewickIO.parse(tree_string, FelTree.NewickTree)
tip_names = [tip.get_name() for tip in tree.gen_tips()]
if len(tip_names) < 4:
raise HandlingError(
'expected at least four tips '
'but found ' + str(len(tip_names)))
if any(name is None for name in tip_names):
raise HandlingError('each terminal node must be labeled')
if len(set(tip_names)) != len(tip_names):
raise HandlingError('each terminal node label must be unique')
trees.append(tree)
# create the response
out = StringIO()
same_count = 0
diff_count = 0
for tree in trees:
# make the local paragraph that will be shown if there is an event
local_out = StringIO()
has_event = False
# print the tree
print >> local_out, NewickIO.get_newick_string(tree)
# get the tip nodes and the internal nodes
tip_nodes = []
internal_nodes = []
for node in tree.preorder():
if node.is_tip():
tip_nodes.append(node)
else:
internal_nodes.append(node)
all_nodes = tip_nodes + internal_nodes
# get all tip name partitions implied by the tree topology
valid_partitions = TreeComparison.get_partitions(tree)
# get results from the augmented distance matrix
D_full = tree.get_partial_distance_matrix(
[id(node) for node in all_nodes])
y_full = get_vector(D_full).tolist()
y = y_full[:len(tip_nodes)]
name_selection = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y) if elem > 0)
name_complement = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y) if elem <= 0)
name_partition_a = frozenset((name_selection, name_complement))
if name_partition_a not in valid_partitions:
print >> local_out, 'augmented distance matrix split fail:',
print >> local_out, name_partition_a
has_event = True
# get results from the not-augmented distance matrix
D = tree.get_partial_distance_matrix([id(node) for node in tip_nodes])
y = get_vector(D).tolist()
name_selection = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y) if elem > 0)
name_complement = frozenset(node.get_name()
for node, elem in zip(tip_nodes, y) if elem <= 0)
name_partition_b = frozenset((name_selection, name_complement))
if name_partition_b not in valid_partitions:
print >> local_out, 'not-augmented distance matrix split fail:',
print >> local_out, name_partition_b
has_event = True
# compare the name partitions
if name_partition_a == name_partition_b:
same_count += 1
else:
diff_count += 1
print >> local_out, 'this tree was split differently '
print >> local_out, 'by the different methods:'
print >> local_out, 'augmented distance matrix split:',
print >> local_out, name_partition_a
print >> local_out, 'not-augmented distance matrix split:',
print >> local_out, name_partition_b
has_event = True
# print a newline between trees
if has_event:
print >> out, local_out.getvalue()
# write the summary
print >> out, 'for this many trees the same split was found:',
print >> out, same_count
print >> out, 'for this many trees different splits were found:',
print >> out, diff_count
# write the response
return out.getvalue()
