def runTest(self):
ref = dendropy.Tree(stream=StringIO("((t5,t6),((t4,(t2,t1)),t3));"), schema="newick")
taxon_set = ref.taxon_set
encode_splits(ref)
o_tree = dendropy.Tree(stream=StringIO("((t1,t2),((t4,(t5,t6)),t3));"), schema="newick", taxon_set=taxon_set)
encode_splits(o_tree)
self.assertEqual(treecalc.symmetric_difference(o_tree, ref), 2)
def kernelOfTest(self, trees):
expected = trees[-1]
input = trees[:-1]
_LOG.debug('input = %s' % str(input))
output = inplace_strict_consensus_merge(input)
encode_splits(output)
encode_splits(expected)
if symmetric_difference(expected, output) != 0:
self.fail("\n%s\n!=\n%s" % (str(output), str(expected)))
def kernelOfTest(self, trees):
expected = trees[-1]
input = trees[:-1]
_LOG.debug('input = %s' % str(input))
output = inplace_strict_consensus_merge(input)
encode_splits(output)
encode_splits(expected)
if symmetric_difference(expected, output) != 0:
self.fail("\n%s\n!=\n%s" % (str(output), str(expected)))
def runTest(self):
taxon_set = dendropy.TaxonSet([str(i+1) for i in range(5)])
tree_list = dendropy.TreeList(
stream=StringIO("""
(5,((4,3),2),1);
(5,(4,3,2),1);
(5,((4,3),2),1);
(5,(4,3),2,1);
(5,((4,3),2),1);
(5,4,3,2,1);
"""),
schema="newick",
taxon_set=taxon_set)
tree = tree_list[0]
expected_tree = tree_list[1]
treesplit.encode_splits(tree)
all_cm = tree.seed_node.edge.split_bitmask
split_to_target = 0xA
treemanip.collapse_conflicting(tree.seed_node, split_to_target, all_cm)
treesplit.encode_splits(tree)
treesplit.encode_splits(expected_tree)
self.assertEqual(treecalc.symmetric_difference(tree, expected_tree), 0)
tree = tree_list[2]
expected_tree = tree_list[3]
treesplit.encode_splits(tree)
all_cm = tree.seed_node.edge.split_bitmask
split_to_target = 0x3
treemanip.collapse_conflicting(tree.seed_node, split_to_target, all_cm)
treesplit.encode_splits(tree)
treesplit.encode_splits(expected_tree)
self.assertEqual(treecalc.symmetric_difference(tree, expected_tree), 0)
tree = tree_list[4]
expected_tree = tree_list[5]
treesplit.encode_splits(tree)
all_cm = tree.seed_node.edge.split_bitmask
split_to_target = 0x5
treemanip.collapse_conflicting(tree.seed_node, split_to_target, all_cm)
treesplit.encode_splits(tree)
treesplit.encode_splits(expected_tree)
self.assertEqual(treecalc.symmetric_difference(tree, expected_tree), 0)
def runTest(self):
ref = dendropy.Tree(stream=StringIO("((t5,t6),((t4,(t2,t1)),t3));"),
schema="newick")
taxon_set = ref.taxon_set
encode_splits(ref)
o_tree = dendropy.Tree(stream=StringIO("((t1,t2),((t4,(t5,t6)),t3));"),
schema="newick",
taxon_set=taxon_set)
encode_splits(o_tree)
self.assertEqual(treecalc.symmetric_difference(o_tree, ref), 2)
def compare_trees(tree_filename1, tree_filename2):
from dendropy import Tree, TreeList
from dendropy.treecalc import symmetric_difference, euclidean_distance, robinson_foulds_distance as rbd, PatristicDistanceMatrix as pdm
c = TreeList([g(tree_filename1), g(tree_filename2)])
pp1 = pdm(c[0]).distances()
pp2 = pdm(c[1]).distances()
sumbl1 = sum(n.edge_length for n in c[0].nodes() if n.edge_length is not None)
sumbl2 = sum(n.edge_length for n in c[1].nodes() if n.edge_length is not None)
e = [n.edge_length for n in c[0].nodes() if n.edge_length is not None]
return {'nBSD':euclidean_distance(c[0], c[1]), 'SDD':symmetric_difference(c[0], c[1]), 'RBD':rbd(c[0], c[1]), 'edgeDelta1': max(pp1)-min(pp1), 'edgeStd1': np.std(pp1),\
'edgeDelta2': max(pp2)-min(pp2), 'edgeStd2': np.std(pp2), 'SumBranchLen1': sumbl1, 'SumBranchLen2': sumbl2}
def testConsensus(self):
con_tree = self.tree_list.consensus(min_freq=0.50, trees_splits_encoded=False, support_label_decimals=2)
con_tree.update_splits()
self.assertEqual(treecalc.symmetric_difference(self.mb_con_tree, con_tree), 0)
self.assertEqual(len(con_tree.split_edges), len(self.mb_con_tree.split_edges))
sd = self.tree_list.split_distribution
for split in self.mb_con_tree.split_edges:
edge1 = self.mb_con_tree.split_edges[split]
edge2 = con_tree.split_edges[split]
if edge1.head_node.label and edge2.head_node.label:
s1 = float(edge1.head_node.label)
s2 = round(float(edge2.head_node.label), 2)
self.assertAlmostEqual(s1, s2, 2)
def runTest(self):
n = '(Basichlsac,(Lamprothma,Mougeotisp),(((Haplomitr2,Petalaphy),((Angiopteri,(((Azollacaro,((Dennstasam,(Oleandrapi,Polypodapp)),Dicksonant)),Vittarifle),Botrychbit)),(Isoetesmel,((((Agathismac,Agathisova),Pseudotsu),(((Libocedrus,Juniperusc),Callitris),Athrotaxi)),((Liriodchi,Nelumbo),Sagittari))))),Thuidium));'
k = dendropy.TreeList(stream=StringIO(n), schema="newick")[0]
trees = dendropy.TreeList(stream=StringIO(n+n), schema="newick", encode_splits=True, taxon_set=k.taxon_set)
ref = trees[0]
changing = trees[1]
rng = RepeatedRandom()
for i in xrange(50):
treemanip.randomly_reorient_tree(changing, rng=rng, splits=True)
self.assertNotEqual(str(changing), n)
changing.debug_check_tree(logger_obj=_LOG, splits=True)
if treecalc.symmetric_difference(ref, changing) != 0:
self.fail("\n%s\n!=\n%s" % (str(ref), str(changing)))
def unique_trees(tree_list, mcmc_trees, format, burnin=0, taxonset=None):
'''Takes a list and a Mr. Bayes mcmc sample as input. Returns
a list of non-redundant tree topologies using symmetric difference,
and the number of redundant topologies in the sample.'''
redundant_count = 0
for tree in tree_iter(mcmc_trees, format, burnin, taxonset):
for ut in tree_list:
sd = treecalc.symmetric_difference(tree, ut)
#print sd ## error check
if sd == 0:
redundant_count += 1
break
else:
tree_list.append(tree)
return tree_list, redundant_count
def unique_trees(tree_list,mcmc_trees,format,burnin=0,taxonset=None):
'''Takes a list and a Mr. Bayes mcmc sample as input. Returns
a list of non-redundant tree topologies using symmetric difference,
and the number of redundant topologies in the sample.'''
redundant_count = 0
for tree in tree_iter(mcmc_trees,format,burnin,taxonset):
for ut in tree_list:
sd = treecalc.symmetric_difference(tree,ut)
#print sd ## error check
if sd == 0:
redundant_count +=1
break
else:
tree_list.append(tree)
return tree_list, redundant_count
def print_distances(tree_list,mle,uniq_flag=False):
mle_tree, taxa = get_mle_tree(mle)
distances = []
uniq_trees = dendropy.TreeList()
count = 1
for t in tree_source_iter(stream=open(tree_list, 'rU'),schema='nexus',taxon_set=taxa):
dist = treecalc.symmetric_difference(mle_tree, t)
print "Distance between MLE tree and tree %i: %i" % (count,dist)
distances.append(dist)
count +=1
if uniq_flag and dist > 0:
uniq_trees.append(t)
print("Mean symmetric distance between MLE and tree list: %d" \
% float(sum(distances)/len(distances)))
return uniq_trees, len(uniq_trees)
def long_branch_symmdiff(trees_to_compare,
edge_len_threshold,
copy_trees=False,
rooted=False):
"""Returns matrix of the symmetric_differences between trees after all
internal edges with lengths < `edge_len_threshold` have been collapsed.
If `copy_trees` is True then the trees will be copied first (if False, then
the trees may will have their short edges collapsed on exit).
"""
if copy_trees:
tree_list = [copy.copy(i) for i in trees_to_compare]
else:
tree_list = list(trees_to_compare)
n_trees = len(tree_list)
_LOG.debug('%d Trees to compare:\n%s\n' %
(n_trees, '\n'.join([str(i) for i in tree_list])))
if n_trees < 2:
return [0 for t in tree_list]
f_r = []
for tree in tree_list:
to_collapse = []
encode_splits(tree)
for edge in tree.preorder_edge_iter(filter_fn=Edge.is_internal):
elen = edge.length
if elen is not None and elen < edge_len_threshold:
to_collapse.append(edge)
for edge in to_collapse:
collapse_edge(edge)
f_r.append(tree.is_rooted)
tree.is_rooted = bool(rooted)
encode_splits(tree)
sd_row = [0] * n_trees
sd_mat = [list(sd_row) for i in xrange(n_trees)]
for i, tree_one in enumerate(tree_list[:-1]):
for col_count, tree_two in enumerate(tree_list[1 + i:]):
j = i + 1 + col_count
sd = symmetric_difference(tree_one, tree_two)
sd_mat[i][j] = sd
sd_mat[j][i] = sd
if not copy_trees:
for r, tree in itertools.izip(f_r, tree_list):
tree.is_rooted = r
return sd_mat
def print_distances(tree_list, mle, uniq_flag=False):
mle_tree, taxa = get_mle_tree(mle)
distances = []
uniq_trees = dendropy.TreeList()
count = 1
for t in tree_source_iter(stream=open(tree_list, 'rU'),
schema='nexus',
taxon_set=taxa):
dist = treecalc.symmetric_difference(mle_tree, t)
print "Distance between MLE tree and tree %i: %i" % (count, dist)
distances.append(dist)
count += 1
if uniq_flag and dist > 0:
uniq_trees.append(t)
print("Mean symmetric distance between MLE and tree list: %d" \
% float(sum(distances)/len(distances)))
return uniq_trees, len(uniq_trees)
def testConsensus(self):
con_tree = self.tree_list.consensus(min_freq=0.50,
trees_splits_encoded=False,
support_label_decimals=2)
con_tree.update_splits()
self.assertEqual(
treecalc.symmetric_difference(self.mb_con_tree, con_tree), 0)
self.assertEqual(len(con_tree.split_edges),
len(self.mb_con_tree.split_edges))
sd = self.tree_list.split_distribution
for split in self.mb_con_tree.split_edges:
edge1 = self.mb_con_tree.split_edges[split]
edge2 = con_tree.split_edges[split]
if edge1.head_node.label and edge2.head_node.label:
s1 = float(edge1.head_node.label)
s2 = round(float(edge2.head_node.label), 2)
self.assertAlmostEqual(s1, s2, 2)
def long_branch_symmdiff(trees_to_compare, edge_len_threshold, copy_trees=False, rooted=False):
"""Returns matrix of the symmetric_differences between trees after all
internal edges with lengths < `edge_len_threshold` have been collapsed.
If `copy_trees` is True then the trees will be copied first (if False, then
the trees may will have their short edges collapsed on exit).
"""
if copy_trees:
tree_list = [copy.copy(i) for i in trees_to_compare]
else:
tree_list = list(trees_to_compare)
n_trees = len(tree_list)
_LOG.debug('%d Trees to compare:\n%s\n' % (n_trees, '\n'.join([str(i) for i in tree_list])))
if n_trees < 2:
return [0 for t in tree_list]
f_r = []
for tree in tree_list:
to_collapse = []
encode_splits(tree)
for edge in tree.preorder_edge_iter(filter_fn=Edge.is_internal):
elen = edge.length
if elen is not None and elen < edge_len_threshold:
to_collapse.append(edge)
for edge in to_collapse:
collapse_edge(edge)
f_r.append(tree.is_rooted)
tree.is_rooted = bool(rooted)
encode_splits(tree)
sd_row = [0]*n_trees
sd_mat = [list(sd_row) for i in xrange(n_trees)]
for i, tree_one in enumerate(tree_list[:-1]):
for col_count, tree_two in enumerate(tree_list[1+i:]):
j = i + 1 + col_count
sd = symmetric_difference(tree_one, tree_two)
sd_mat[i][j] = sd
sd_mat[j][i] = sd
if not copy_trees:
for r, tree in itertools.izip(f_r, tree_list):
tree.is_rooted = r
return sd_mat
def compare_trees(tree_filename1, tree_filename2): from dendropy import Tree, TreeList from dendropy.treecalc import symmetric_difference g = lambda x: Tree.get_from_path(x, 'newick') c = TreeList([g(tree_filename1), g(tree_filename2)]) return symmetric_difference(c[0], c[1])
#! /usr/bin/env python
import dendropy
from dendropy import multi_tree_source_iter
from dendropy import treecalc
distances = []
taxa = dendropy.TaxonSet()
mle_tree = dendropy.Tree.get_from_path('pythonidae.mle.nex',
'nexus',
taxon_set=taxa)
mcmc_tree_file_paths = [
'pythonidae.mb.run1.t', 'pythonidae.mb.run2.t', 'pythonidae.mb.run3.t',
'pythonidae.mb.run4.t'
]
for mcmc_tree in multi_tree_source_iter(mcmc_tree_file_paths,
schema='nexus',
taxon_set=taxa):
distances.append(treecalc.symmetric_difference(mle_tree, mcmc_tree))
print("Mean symmetric distance between MLE and MCMC trees: %d" %
float(sum(distances) / len(distances)))
#! /usr/bin/env python
import dendropy
from dendropy import tree_source_iter
from dendropy import treecalc
distances = []
taxa = dendropy.TaxonSet()
mle_tree = dendropy.Tree.get_from_path('pythonidae.mle.nex', 'nexus', taxon_set=taxa)
for mcmc_tree in tree_source_iter(
stream=open('pythonidae.mcmc.nex', 'rU'),
schema='nexus',
taxon_set=taxa,
tree_offset=200):
distances.append(treecalc.symmetric_difference(mle_tree, mcmc_tree))
print("Mean symmetric distance between MLE and MCMC trees: %d"
% float(sum(distances)/len(distances)))
def symmetric_difference(tree_str1, tree_str2): if tree_str1 is None or tree_str2 is None or "" == tree_str1 or "" == tree_str2: return -1 taxon = TaxonSet() return treecalc.symmetric_difference(Tree(stream=StringIO(tree_str1), schema='newick', taxon_set=taxon), Tree(stream=StringIO(tree_str2), schema='newick', taxon_set=taxon))
def compare_trees(tree_filename1, tree_filename2):
from dendropy import Tree, TreeList
from dendropy.treecalc import symmetric_difference, euclidean_distance, robinson_foulds_distance as rbd
c = TreeList([g(tree_filename1), g(tree_filename2)])
return {'nBSD':euclidean_distance(c[0],c[1]), 'SDD':symmetric_difference(c[0], c[1]), \
'RBD':rbd(c[0],c[1])}