def new_clade(self, parent=None, id=None):
"""Returns a new Newick.Clade, optionally with a temporary reference
to its parent clade."""
try:
parentPath = parent.find("property[@ref='Lm:path']").text
except:
# doesn't have a path, means it's the root ?
pass
if parent is not None:
clade = SubElement(parent, "clade", namespace=None)
if id is not None:
SubElement(clade,
"property",
value=id,
namespace=None,
attribs=[('ref', 'Lm:pathId'),
('datatype', 'xsd:integer'),
('applies_to', 'clade')])
path = str(id) + ',' + parentPath
SubElement(clade,
"property",
value=path,
namespace=None,
attribs=[('ref', 'Lm:path'),
('datatype', 'xsd:string'),
('applies_to', 'clade')])
self.parentMap[clade] = parent
#if path is not None:
#SubElement(cladeEl, "path", value=path, namespace=None)
#SubElement(cladeEl, "id", value=id, namespace=None)
#return cladeEl
else:
clade = Element("clade", namespace=None)
# new lines for LmXml SubElement(clade, "property", value=id, namespace=None, attrib={'ref': 'Lm:pathId',
# 'datatype': 'xsd:integer',
# 'applies_to': 'clade'})
SubElement(clade,
"property",
value=id,
namespace=None,
attribs=[('ref', 'Lm:pathId'),
('datatype', 'xsd:integer'),
('applies_to', 'clade')])
SubElement(clade,
"property",
value=id,
namespace=None,
attribs=[('ref', 'Lm:path'), ('datatype', 'xsd:string'),
('applies_to', 'clade')])
#clade = Newick.Clade()
#clade = None
#if parent:
# clade.parent = parent
return clade
def processNexusForPhyloXml(nexStr):
if nexStr.startswith('TREE'):
parts = nexStr.strip('TREE ').split(' = ')
name = parts[0]
phylo = parts[1]
print "name ", name
t = Element(
"phyloxml",
namespace=None,
attribs=
[("xmlns", "http://www.phyloxml.org"),
("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance"),
("xsi:schemaLocation",
"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"
)])
phylogenyEl = SubElement(t,
"phylogeny",
namespace=None,
attribs=[('rooted', 'true')])
SubElement(phylogenyEl, 'name', value=name, namespace=None)
xmlify(phylogenyEl, phylo.strip('[&R] '))
return t
def createClade(parent, depth, name=None):
cladeEl = SubElement(parent, "clade", namespace=None)
SubElement(cladeEl, "branch_length", value=depth, namespace=None)
if name is not None:
SubElement(cladeEl, "name", value=name, namespace=None)
return cladeEl
phylogenyEl = SubElement(t, "phylogeny", namespace=None, attribs=[('rooted', 'true')])
SubElement(phylogenyEl, 'name', value=name, namespace=None)
xmlify(phylogenyEl, phylo.strip('[&R] '))
return t
#outStr = tostring(processNexusForPhyloXml(nexusTree))
t = open('/home/jcavner/PhyloXM_Examples/amphibiansFromNexus.nhx','r').read()
t = nexusTreeMod
sh = Parser.from_string(t) #nexusTreeMod- for bats, works
p = Parser(sh)
eTree,phyloDict,parentDicts = p.parse()
t = Element("phyloxml", namespace=None,
attribs=[
("xmlns", "http://www.phyloxml.org"),
("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance"),
("xsi:schemaLocation", "http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd")
])
phylo = SubElement(t, "phylogeny", namespace=None, attribs=[('rooted', 'false')])
phylo.append(eTree)
outStr = tostring(t)
with open('/home/jcavner/PhyloXM_Examples/nexusTreeMod.xml', 'w') as f:
f.write(outStr)
with open('/home/jcavner/PhyloXM_Examples/amphibianJSONDirectTest.json','w') as f:
f.write(simplejson.dumps(phyloDict,sort_keys=True, indent=4))
def add_name(self, clade, name):
SubElement(clade, "name", name, namespace=None)
#outStr = tostring(processNexusForPhyloXml(nexusTree))
t = open('/home/jcavner/PhyloXM_Examples/amphibiansFromNexus.nhx', 'r').read()
t = nexusTreeMod
sh = Parser.from_string(t) #nexusTreeMod- for bats, works
p = Parser(sh)
eTree, phyloDict, parentDicts = p.parse()
t = Element(
"phyloxml",
namespace=None,
attribs=[
("xmlns", "http://www.phyloxml.org"),
("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance"),
("xsi:schemaLocation",
"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd")
])
phylo = SubElement(t,
"phylogeny",
namespace=None,
attribs=[('rooted', 'false')])
phylo.append(eTree)
outStr = tostring(t)
with open('/home/jcavner/PhyloXM_Examples/nexusTreeMod.xml', 'w') as f:
f.write(outStr)
with open('/home/jcavner/PhyloXM_Examples/amphibianJSONDirectTest.json',
'w') as f:
f.write(simplejson.dumps(phyloDict, sort_keys=True, indent=4))