def testBasicDocumentFromInit(self):
test_dataset = dendropy.DataSet(stream=pathmap.tree_source_stream(
datagen.reference_trees_filename(schema="newick")),
schema="newick")
self.assertDistinctButEqual(self.reference_dataset,
test_dataset,
ignore_taxon_order=True)
def testBasicDocumentParseFromReader(self):
reader = newick.NewickReader()
test_dataset = reader.read(stream=pathmap.tree_source_stream(
datagen.reference_trees_filename(schema="newick")))
self.assertDistinctButEqual(self.reference_dataset,
test_dataset,
ignore_taxon_order=True)
def testReferenceTreeFileDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream(datagen.reference_trees_filename(schema="nexus")), "nexus")
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None)
def testReferenceTreeFileSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-block.nexus"), "nexus", taxon_set=ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testNexusDistinctTaxa(self):
stream = pathmap.tree_source_stream(
datagen.reference_trees_filename(schema="nexus"))
for idx, test_tree in enumerate(
dataio.tree_source_iter(stream=stream, schema='nexus/newick')):
self.assertDistinctButEqualTree(self.ref_tree_list[idx],
test_tree,
distinct_taxa=True)
def testReferenceTreeFileNoTaxaBlockNoTranslateBlockSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
reader = dataio.get_reader("nexus", taxon_set=ref_tree_list.taxon_set)
dataset = reader.read(
stream=pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-no-translate-block.nexus")
)
self.assertEqual(len(dataset.tree_lists), 1)
self.assertDistinctButEqualTreeList(ref_tree_list, dataset.tree_lists[0], distinct_taxa=False, equal_oids=None)
def testReferenceTreeFileNoTaxaBlockNoTranslateBlockDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-no-translate-block.nexus"), "nexus")
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None)
def testReferenceTreeFileNoTaxaBlockDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_stream(
pathmap.tree_source_stream(
"pythonidae.reference-trees.no-taxa-block.nexus"), "nexus")
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_stream(
pathmap.tree_source_stream(
datagen.reference_trees_filename(schema="nexus")), "nexus")
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None)
def test_ultrametric(self):
trees = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.nexus"), "nexus")
for tree in trees:
dists = tree.calc_node_root_distances()
min_dist, max_dist = tree.minmax_leaf_distance_from_root()
trunc_dists = [(max_dist * f) for f in (0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9)]
for td in trunc_dists:
num_lineages = tree.num_lineages_at(td)
self.check_tree(tree, td, num_lineages)
def testReferenceTreeFileNoTaxaBlockNoTranslateBlockSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
reader = dataio.get_reader('nexus', taxon_set=ref_tree_list.taxon_set)
dataset = reader.read(stream=pathmap.tree_source_stream(
"pythonidae.reference-trees.no-taxa-no-translate-block.nexus"))
self.assertEqual(len(dataset.tree_lists), 1)
self.assertDistinctButEqualTreeList(ref_tree_list,
dataset.tree_lists[0],
distinct_taxa=False,
equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
reader = dataio.get_reader('nexus')
dataset = reader.read(stream=pathmap.tree_source_stream(
datagen.reference_trees_filename(schema="nexus")))
self.assertEqual(len(dataset.tree_lists), 1)
self.assertDistinctButEqualTreeList(ref_tree_list,
dataset.tree_lists[0],
distinct_taxa=True,
equal_oids=None)
def testReferenceTreeFileNoTaxaBlockDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
reader = dataio.get_reader('nexus')
dataset = reader.read(stream=pathmap.tree_source_stream("pythonidae.reference-trees.no-taxa-block.nexus"))
self.assertEqual(len(dataset.tree_lists), 1)
self.assertDistinctButEqualTreeList(
ref_tree_list,
dataset.tree_lists[0],
distinct_taxa=True,
equal_oids=None)
def testReferenceTreeFileDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
reader = dataio.get_reader('nexus')
dataset = reader.read(stream=pathmap.tree_source_stream(datagen.reference_trees_filename(schema="nexus")))
self.assertEqual(len(dataset.tree_lists), 1)
self.assertDistinctButEqualTreeList(
ref_tree_list,
dataset.tree_lists[0],
distinct_taxa=True,
equal_oids=None)
def test_ultrametric(self):
trees = dendropy.TreeList.get_from_stream(
pathmap.tree_source_stream("pythonidae.reference-trees.nexus"),
"nexus")
for tree in trees:
dists = tree.calc_node_root_distances()
min_dist, max_dist = tree.minmax_leaf_distance_from_root()
trunc_dists = [(max_dist * f) for f in (0.1, 0.2, 0.3, 0.4, 0.5,
0.6, 0.7, 0.8, 0.9)]
for td in trunc_dists:
num_lineages = tree.num_lineages_at(td)
self.check_tree(tree, td, num_lineages)
def setUp(self):
self.trees = dendropy.TreeList.get_from_stream(pathmap.tree_source_stream("pythonidae.reference-trees.nexus"), "nexus")
def testNewickSameTaxa(self):
stream = pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick"))
for idx, test_tree in enumerate(dataio.tree_source_iter(stream=stream, schema='nexus/newick', taxon_set=self.ref_tree_list.taxon_set)):
self.assertDistinctButEqualTree(self.ref_tree_list[idx], test_tree, distinct_taxa=False)
def testNewickDistinctTaxa(self):
stream = pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick"))
for idx, test_tree in enumerate(dataio.tree_source_iter(stream=stream, schema='nexus/newick')):
self.assertDistinctButEqualTree(self.ref_tree_list[idx], test_tree, distinct_taxa=True, ignore_taxon_order=True)
def main():
tlist = dendropy.TreeList(stream=pathmap.tree_source_stream(datagen.reference_trees_filename("nexus")), schema="nexus")
for idx, t in enumerate(tlist):
t.label = "Tree%02d" % (idx+1)
t.assign_node_labels_from_taxon_or_oid()
result = []
result.append("def reference_tree_list_postorder_node_labels():")
result.append(" return [")
for t in tlist:
nodes = [("'" + nd.label + "'") for nd in t.postorder_node_iter()]
result.append(" [%s]," % (",".join(nodes)))
result.append(" ]")
result.append("")
result.append("def reference_tree_list_newick_string(taxon_set=None):")
result.append(' return """\\')
for t in tlist:
result.append(' %s;' % t.as_newick_string(include_internal_labels=True))
result.append(' """')
result.append("")
result.append("def reference_tree_list_node_relationships():")
result.append(" treelist_node_references = [")
for t in tlist:
result.append(" {")
for nd in t:
if nd.parent_node is not None:
pn_label = "'" + nd.parent_node.label + "'"
else:
pn_label = 'None'
if nd.taxon is not None:
t_label = "'" + nd.taxon.label + "'"
else:
t_label = 'None'
result.append(" '%s' : NodeRelationship(parent_label=%s, child_labels=[%s], edge_length=%s, taxon_label=%s)," % \
(nd.label,
pn_label,
",".join(["'"+c.label+"'" for c in nd.child_nodes()]),
nd.edge.length,
t_label))
result.append(" },")
result.append(" ]")
result.append(" return treelist_node_references")
result.append("")
tree_list_name = 'tree_list'
src_lines = tlist.as_python_source(tree_list_name=tree_list_name, oids=True).split("\n")
result.append("def reference_tree_list(taxon_set=None):")
src_lines[0] = re.sub("(dendropy\.TreeList\(label\=.*)\)", "\g<1>, taxon_set=taxon_set)", src_lines[0])
for s in src_lines:
result.append(" %s" % s)
result.append("""\
# set labels of nodes with taxa to taxon label, else oid (for consistent
# identification in debugging)
for t in %s:
t.assign_node_labels_from_taxon_or_oid()
return %s
""" % (tree_list_name, tree_list_name))
result.append("")
sys.stdout.write("\n".join(result))
def setUp(self):
s = pathmap.tree_source_stream("pythonidae.annotated.nexml")
self.dataset = dendropy.DataSet.get_from_stream(s, "nexml")
def testReadSummaryTree(self):
tree = dendropy.Tree.get_from_stream(pathmap.tree_source_stream('pythonidae.beast.summary.tre'), 'beast-summary-tree')
self.verify_node_info(tree)
def testBasicDocumentFromInit(self):
test_dataset = dendropy.DataSet(stream=pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick")), schema="newick")
self.assertDistinctButEqual(self.reference_dataset, test_dataset, ignore_taxon_order=True)
def testBasicDocumentParseFromReader(self):
reader = newick.NewickReader()
test_dataset = reader.read(stream=pathmap.tree_source_stream(datagen.reference_trees_filename(schema="newick")))
self.assertDistinctButEqual(self.reference_dataset, test_dataset, ignore_taxon_order=True)
def setUp(self):
self.trees = dendropy.TreeList.get_from_stream(
pathmap.tree_source_stream("pythonidae.reference-trees.nexus"),
"nexus")
def testParseNexmlAnnotations(self):
s = pathmap.tree_source_stream("treebase_s373.xml")
dataset = dendropy.DataSet(stream=s, schema="nexml")
self.verify_dataset(dataset)
def testSummaryTreeIter(self):
stream = pathmap.tree_source_stream('pythonidae.beast.summary.tre')
for tree in dendropy.tree_source_iter(stream, 'beast-summary-tree'):
self.verify_node_info(tree)
def testParseNexmlAnnotations(self):
s = pathmap.tree_source_stream("treebase_s373.xml")
dataset = dendropy.DataSet(stream=s, schema="nexml")
self.verify_dataset(dataset)
def main():
tlist = dendropy.TreeList(stream=pathmap.tree_source_stream(
datagen.reference_trees_filename("nexus")),
schema="nexus")
for idx, t in enumerate(tlist):
t.label = "Tree%02d" % (idx + 1)
t.assign_node_labels_from_taxon_or_oid()
result = []
result.append("def reference_tree_list_postorder_node_labels():")
result.append(" return [")
for t in tlist:
nodes = [("'" + nd.label + "'") for nd in t.postorder_node_iter()]
result.append(" [%s]," % (",".join(nodes)))
result.append(" ]")
result.append("")
result.append("def reference_tree_list_newick_string(taxon_set=None):")
result.append(' return """\\')
for t in tlist:
result.append(' %s;' %
t.as_newick_string(include_internal_labels=True))
result.append(' """')
result.append("")
result.append("def reference_tree_list_node_relationships():")
result.append(" treelist_node_references = [")
for t in tlist:
result.append(" {")
for nd in t:
if nd.parent_node is not None:
pn_label = "'" + nd.parent_node.label + "'"
else:
pn_label = 'None'
if nd.taxon is not None:
t_label = "'" + nd.taxon.label + "'"
else:
t_label = 'None'
result.append(" '%s' : NodeRelationship(parent_label=%s, child_labels=[%s], edge_length=%s, taxon_label=%s)," % \
(nd.label,
pn_label,
",".join(["'"+c.label+"'" for c in nd.child_nodes()]),
nd.edge.length,
t_label))
result.append(" },")
result.append(" ]")
result.append(" return treelist_node_references")
result.append("")
tree_list_name = 'tree_list'
src_lines = tlist.as_python_source(tree_list_name=tree_list_name,
oids=True).split("\n")
result.append("def reference_tree_list(taxon_set=None):")
src_lines[0] = re.sub("(dendropy\.TreeList\(label\=.*)\)",
"\g<1>, taxon_set=taxon_set)", src_lines[0])
for s in src_lines:
result.append(" %s" % s)
result.append("""\
# set labels of nodes with taxa to taxon label, else oid (for consistent
# identification in debugging)
for t in %s:
t.assign_node_labels_from_taxon_or_oid()
return %s
""" % (tree_list_name, tree_list_name))
result.append("")
sys.stdout.write("\n".join(result))