def testMixedNexusAndNewickSameTaxa(self):
filenames = [datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
for idx, test_tree in enumerate(dataio.multi_tree_source_iter(filepaths, schema="nexus/newick", taxon_set=taxon_set)):
self.assertDistinctButEqualTree(self.next_ref_tree(), test_tree, distinct_taxa=False, ignore_taxon_order=True)
self.assertEqual(idx, 43)
def testBurnIn(self):
filenames = [datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
self.ref_index = 5
for idx, test_tree in enumerate(dataio.multi_tree_source_iter(filepaths,
schema="nexus/newick",
taxon_set=taxon_set,
tree_offset=5)):
check_tree = self.next_ref_tree(restart_index=5)
self.assertDistinctButEqualTree(check_tree, test_tree, distinct_taxa=False, ignore_taxon_order=True)
self.assertEqual(idx, 23)
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 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 testFromFileFactoryDistinctTaxa(self):
tree_list = datagen.reference_tree_list()
s = pathmap.tree_source_path(
datagen.reference_trees_filename(schema="nexus"))
tree = dendropy.Tree.get_from_stream(open(s, "rU"),
"nexus",
tree_offset=2)
self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=True)
def testReferenceTreeFileDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_path(pathmap.tree_source_path(datagen.reference_trees_filename(schema="newick")), 'newick')
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None,
ignore_taxon_order=True)
def testMixedNexusAndNewickSameTaxa(self):
filenames = [
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")
]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
for idx, test_tree in enumerate(
dataio.multi_tree_source_iter(filepaths,
schema="nexus/newick",
taxon_set=taxon_set)):
self.assertDistinctButEqualTree(self.next_ref_tree(),
test_tree,
distinct_taxa=False,
ignore_taxon_order=True)
self.assertEqual(idx, 43)
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 testFromPathFactorySameTaxa(self):
tree_list = datagen.reference_tree_list()
s = pathmap.tree_source_path(
datagen.reference_trees_filename(schema="nexus"))
tree = dendropy.Tree.get_from_path(s,
"nexus",
tree_offset=2,
taxon_set=tree_list.taxon_set)
self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=False)
def testReferenceTreeFileDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_path(
pathmap.tree_source_path(
datagen.reference_trees_filename(schema="newick")), 'newick')
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None,
ignore_taxon_order=True)
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 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 testReferenceTreeFileSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_path(pathmap.tree_source_path(datagen.reference_trees_filename(schema="newick")),
'newick',
taxon_set=ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testReferenceTreeFileSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
t_tree_list = dendropy.TreeList.get_from_path(
pathmap.tree_source_path(
datagen.reference_trees_filename(schema="newick")),
'newick',
taxon_set=ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testBurnIn(self):
filenames = [
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")
]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
self.ref_index = 5
for idx, test_tree in enumerate(
dataio.multi_tree_source_iter(filepaths,
schema="nexus/newick",
taxon_set=taxon_set,
tree_offset=5)):
check_tree = self.next_ref_tree(restart_index=5)
self.assertDistinctButEqualTree(check_tree,
test_tree,
distinct_taxa=False,
ignore_taxon_order=True)
self.assertEqual(idx, 23)
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 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 testFromPathFactoryDistinctTaxa(self):
tree_list1 = datagen.reference_tree_list()
s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus"))
tree_list2 = dendropy.TreeList.get_from_path(s, "nexus")
self.assertDistinctButEqual(tree_list1, tree_list2, distinct_taxa=True)
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 testFromPathFactorySameTaxa(self):
tree_list = datagen.reference_tree_list()
s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus"))
tree = dendropy.Tree.get_from_path(s, "nexus", tree_offset=2, taxon_set=tree_list.taxon_set)
self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=False)
def testFromFileFactoryDistinctTaxa(self):
tree_list = datagen.reference_tree_list()
s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus"))
tree = dendropy.Tree.get_from_stream(open(s, "rU"), "nexus", tree_offset=2)
self.assertDistinctButEqual(tree_list[2], tree, distinct_taxa=True)
def testFromPathFactoryDistinctTaxa(self):
tree_list1 = datagen.reference_tree_list()
s = pathmap.tree_source_path(datagen.reference_trees_filename(schema="nexus"))
tree_list2 = dendropy.TreeList.get_from_path(s, "nexus")
self.assertDistinctButEqual(tree_list1, tree_list2, distinct_taxa=True)
