from ete3 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>
def _generate_internal_node_name(self, tree):
if self.use_internal_name is False:
for node in tree.traverse("postorder"):
if node.is_leaf() is False:
self.set_taxon_name(node)
if self.tree_format == 'phyloxml':
#### IMPORTANT ####
'''
This code section is an horrible fix due to incompatibility of Phyloxml().export() with python3.
We overwrite the export module (and its functions) here to deal with both byte and unicode.
TODO: this should be replace as ASAP
'''
def showIndent(outfile, level):
for idx in range(level):
g = ' '
g = g.encode('UTF-8')
outfile.write(g)
namespace_ = 'phy:'
name_ = 'Phyloxml'
namespacedef_ = ''
outfile = BytesIO()
level = 0
def export(xxxx,
outfile,
level,
namespace_='phy:',
name_='Phyloxml',
namespacedef_=''):
showIndent(outfile, level)
x = '<%s%s%s' % (
namespace_,
name_,
namespacedef_ and ' ' + namespacedef_ or '',
)
x = x.encode('UTF-8')
outfile.write(x)
already_processed = []
exportAttributes(xxxx,
outfile,
level,
already_processed,
namespace_,
name_='Phyloxml')
if hasContent_(xxxx):
y = '>\n'
y = y.encode('UTF-8')
outfile.write(y)
exportChildren(xxxx, outfile, level + 1, namespace_, name_)
showIndent(outfile, level)
z = '</%s%s>\n' % (namespace_, name_)
z = z.encode('UTF-8')
outfile.write(z)
else:
v = '/>\n'
v = v.encode('UTF-8')
outfile.write(v)
def exportAttributes(xxxx,
outfile,
level,
already_processed,
namespace_='phy:',
name_='Phyloxml'):
pass
def exportChildren(xxxx,
outfile,
level,
namespace_='phy:',
name_='Phyloxml',
fromsubclass_=False):
for phylogeny_ in xxxx.phylogeny:
export(phylogeny_,
outfile,
level,
namespace_,
name_='phylogeny')
def hasContent_(xxxx):
if hasattr(xxxx, 'phylogeny'):
return True
else:
return False
#### IMPORTANT ####
# build phyloxml project
project = Phyloxml()
project.add_phylogeny(tree)
# Export phyloxml document
export(project,
outfile,
level,
namespace_='phy:',
name_='Phyloxml',
namespacedef_='')
OUTPUT = outfile
# Some ad-hoc changes to the phyloxml formatted document to meet the schema definition
text = OUTPUT.read().decode('UTF-8')
text = text.replace('phy:', '')
text = re.sub('branch_length_attr="[^"]+"', "", text)
header = """
<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.20/phyloxml.xsd">
"""
text = re.sub('<Phyloxml[^>]+>', header, text)
text = text.replace('Phyloxml', 'phyloxml')
text = text.replace('\n', '').replace("'", '')
self.tree_str = text
else:
self.tree_str = self.tree.write(format=8, format_root_node=True)
from ete3 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">
