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from ete3 import Phyloxml
project = Phyloxml()
project.build_from_file("apaf.xml")
# Each tree contains the same methods as a PhyloTree object
for tree in project.get_phylogeny():
print tree
# you can even use rendering options
tree.show()
# PhyloXML features are stored in the phyloxml_clade attribute
for node in tree:
print "Node name:", node.name
for seq in node.phyloxml_clade.get_sequence():
for domain in seq.domain_architecture.get_domain():
domain_data = [domain.valueOf_, domain.get_from(), domain.get_to()]
print " Domain:", '\t'.join(map(str, domain_data))
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