from ete_dev import Phyloxml, phyloxml
import random
project = Phyloxml()
# Creates a random tree
phylo = phyloxml.PhyloxmlTree()
phylo.populate(5, random_branches=True)
phylo.phyloxml_phylogeny.set_name("test_tree")
# Add the tree to the phyloxml project
project.add_phylogeny(phylo)
print project.get_phylogeny()[0]
# /-iajom
# /---|
# | \-wiszh
#----|
# | /-xrygw
# \---|
# | /-gjlwx
# \---|
# \-ijvnk
# Trees can be operated as normal ETE trees
phylo.show()
# Export the project as phyloXML format
project.export()
# <phy:Phyloxml xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd">
from ete_dev 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))
from ete_dev import Phyloxml, phyloxml
import random
project = Phyloxml()
# Creates a random tree
phylo = phyloxml.PhyloxmlTree()
phylo.populate(5, random_branches=True)
phylo.phyloxml_phylogeny.set_name("test_tree")
# Add the tree to the phyloxml project
project.add_phylogeny(phylo)
print project.get_phylogeny()[0]
# /-iajom
# /---|
# | \-wiszh
#----|
# | /-xrygw
# \---|
# | /-gjlwx
# \---|
# \-ijvnk
# Trees can be operated as normal ETE trees
phylo.show()
# Export the project as phyloXML format
project.export()
# <phy:Phyloxml xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd">
# <phy:phylogeny>