def other(self, elem, namespace, localtag):
return PX.Other(localtag,
namespace,
elem.attrib,
value=elem.text and elem.text.strip() or None,
children=[
self.other(child, *_split_namespace(child.tag))
for child in elem
])
def other(self, elem, namespace, localtag):
"""Create an Other object, a non-phyloXML element."""
return PX.Other(localtag,
namespace,
elem.attrib,
value=elem.text and elem.text.strip() or None,
children=[
self.other(child, *_split_namespace(child.tag))
for child in elem
])
def main():
##################### get parser ###############################
parser = get_parser()
######## Print parser help if arguments missed #################
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
########### Manage workflow accorded to Args ##################
Arguments = parser.parse_args()
# parser = etree.XMLParser(remove_blank_text=True)
# xmlfile = Arguments.xml
# tree = etree.ElementTree()
# tree =etree.parse(xmlfile,parser)
# print tree
# root = tree.getroot()
# print root
# test = root.xpath("phylogeny")
# print test
# for var in test :
# toto = var.findall("clade")[0]
# print toto.text
# print var
tree = Phylo.read("jpp2.xml", 'phyloxml')
for clade in tree.find_clades(name=True):
clade.other = [
PhyloXML.Other(tag="annotation",
namespace="",
children=[
PhyloXML.Other('desc', value='youpi'),
PhyloXML.Other('uri', value='http://lol.com')
])
]
clade.annotation = PhyloXML.Annotation(desc="youpi",
uri="http://lol.com")
Phylo.write(tree, "jpp.xml", 'phyloxml')
