from ete3 import Nexml
# Create an empty Nexml project
nexml_project = Nexml()
# Load content from NeXML file
nexml_project.build_from_file("trees.xml")
# All XML elements are within the project instance.
# exist in each element to access their attributes.
print "Loaded Taxa:"
for taxa in nexml_project.get_otus():
for otu in taxa.get_otu():
print "OTU:", otu.id
# Extracts all the collection of trees in the project
tree_collections = nexml_project.get_trees()
# Select the first collection
collection_1 = tree_collections[0]
# print the topology of every tree
for tree in collection_1.get_tree():
# trees contain all the nexml information in their "nexml_node",
# "nexml_tree", and "nexml_edge" attributes.
print "Tree id", tree.nexml_tree.id
print tree
for node in tree.traverse():
print "node", node.nexml_node.id, "is associated with", node.nexml_node.otu, "OTU"
# Output:
# ==========
# Loaded Taxa:
