def write(obj, file, encoding=DEFAULT_ENCODING, indent=True):
"""Write a phyloXML file.
:Parameters:
obj
an instance of `Phyloxml`, `Phylogeny` or `BaseTree.Tree`, or an
iterable of either of the latter two. The object will be converted
to a Phyloxml object before serialization.
file
either an open handle or a file name.
"""
def fix_single(tree):
if isinstance(tree, PX.Phylogeny):
return tree
if isinstance(tree, PX.Clade):
return tree.to_phylogeny()
if isinstance(tree, PX.BaseTree.Tree):
return PX.Phylogeny.from_tree(tree)
if isinstance(tree, PX.BaseTree.Clade):
return PX.Phylogeny.from_tree(PX.BaseTree.Tree(root=tree))
else:
raise ValueError("iterable must contain Tree or Clade types")
if isinstance(obj, PX.Phyloxml):
pass
elif isinstance(obj, (PX.BaseTree.Tree, PX.BaseTree.Clade)):
obj = fix_single(obj).to_phyloxml()
elif hasattr(obj, '__iter__'):
obj = PX.Phyloxml({}, phylogenies=(fix_single(t) for t in obj))
else:
raise ValueError("First argument must be a Phyloxml, Phylogeny, "
"Tree, or iterable of Trees or Phylogenies.")
return Writer(obj).write(file, encoding=encoding, indent=indent)
def read(self):
"""Parse the phyloXML file and create a single Phyloxml object."""
phyloxml = PX.Phyloxml({_local(key): val for key, val in self.root.items()})
other_depth = 0
for event, elem in self.context:
namespace, localtag = _split_namespace(elem.tag)
if event == "start":
if namespace != NAMESPACES["phy"]:
other_depth += 1
continue
if localtag == "phylogeny":
phylogeny = self._parse_phylogeny(elem)
phyloxml.phylogenies.append(phylogeny)
if event == "end" and namespace != NAMESPACES["phy"]:
# Deal with items not specified by phyloXML
other_depth -= 1
if other_depth == 0:
# We're directly under the root node -- evaluate
otr = self.other(elem, namespace, localtag)
phyloxml.other.append(otr)
self.root.clear()
return phyloxml
