from ete2 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:
# ==========
from ete2 import Nexml
# Creates and empty NeXML project
p = Nexml()
# Fill it with the tolweb example
p.build_from_file("tolweb.xml")
# extract the first collection of trees
tree_collection = p.trees[0]
# and all the tree instances in it
trees = tree_collection.tree
# For each loaded tree, prints its structure and some of its
# meta-properties
for t in trees:
print t
print
print "Leaf node meta information:\n"
print
for meta in t.children[0].nexml_node.meta:
print meta.property, ":", (meta.content)
# Output
# ==========
#
# ---- /-node3(Eurysphindus)
#
# Leaf node meta information:
#
#
'--dpi',
nargs=1,
default=[300],
type=int,
help='The dots-per-inch (DPI) in the output file.'
)
args = argparser.parse_args()
# Change single-list items into single items.
args.output = args.output[0]
args.dpi = args.dpi[0]
args.width = args.width[0]
args.height = args.height[0]
args.source = args.source[0]
nexml = Nexml()
nexml.build_from_file(args.source)
def build_tree_style(tree):
# use our simple TSS cascade to prepare an ETE TreeStyle object
sheets = gather_tss_stylesheets(tree)
if len(sheets) == 0:
return None
# Some styles can be applied to the entire tree
ts = TreeStyle()
# For nodes (and other elements?), build an ordered set of TSS rules
# to apply to each element in our layout function
node_rules = []
for s in sheets: