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# Copyright (C) 2013 by Ben Morris ([email protected])
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox
# and Bio.Phylo.Newick, copyright 2009 by Eric Talevich.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""I/O function wrappers for the NeXML file format.
See: http://www.nexml.org
"""
from io import StringIO
from xml.dom import minidom
from xml.etree import ElementTree
from Bio.Phylo import NeXML
from ._cdao_owl import cdao_elements, cdao_namespaces, resolve_uri
NAMESPACES = {
"xsi": "http://www.w3.org/2001/XMLSchema-instance",
"xml": "http://www.w3.org/XML/1998/namespace",
"nex": "http://www.nexml.org/2009",
"xsd": "http://www.w3.org/2001/XMLSchema#",
}
NAMESPACES.update(cdao_namespaces)
DEFAULT_NAMESPACE = NAMESPACES["nex"]
VERSION = "0.9"
SCHEMA = "http://www.nexml.org/2009/nexml/xsd/nexml.xsd"
try:
register_namespace = ElementTree.register_namespace
except AttributeError:
if not hasattr(ElementTree, "_namespace_map"):
# cElementTree needs the pure-Python xml.etree.ElementTree
from xml.etree import ElementTree as ET_py
ElementTree._namespace_map = ET_py._namespace_map
def register_namespace(prefix, uri):
"""Set NameSpace map."""
ElementTree._namespace_map[uri] = prefix
for prefix, uri in NAMESPACES.items():
register_namespace(prefix, uri)
def qUri(s):
"""Given a prefixed URI, return the full URI."""
return resolve_uri(s, namespaces=NAMESPACES, xml_style=True)
def cdao_to_obo(s):
"""Optionally converts a CDAO-prefixed URI into an OBO-prefixed URI."""
return f"obo:{cdao_elements[s[len('cdao:'):]]}"
def matches(s):
"""Check for matches in both CDAO and OBO namespaces."""
if s.startswith("cdao:"):
return (s, cdao_to_obo(s))
else:
return (s,)
class NeXMLError(Exception):
"""Exception raised when NeXML object construction cannot continue."""
pass
# ---------------------------------------------------------
# Public API
def parse(handle, **kwargs):
"""Iterate over the trees in a NeXML file handle.
:returns: generator of Bio.Phylo.NeXML.Tree objects.
"""
return Parser(handle).parse(**kwargs)
def write(trees, handle, plain=False, **kwargs):
"""Write a trees in NeXML format to the given file handle.
:returns: number of trees written.
"""
return Writer(trees).write(handle, plain=plain, **kwargs)
# ---------------------------------------------------------
# Input
class Parser:
"""Parse a NeXML tree given a file handle.
Based on the parser in ``Bio.Nexus.Trees``.
"""
def __init__(self, handle):
"""Initialize parameters for NeXML file parser."""
self.handle = handle
@classmethod
def from_string(cls, treetext):
"""Convert file handle to StringIO object."""
handle = StringIO(treetext)
return cls(handle)
def add_annotation(self, node_dict, meta_node):
"""Add annotations for the NeXML parser."""
if "property" in meta_node.attrib:
prop = meta_node.attrib["property"]
else:
prop = "meta"
if prop in matches("cdao:has_Support_Value"):
node_dict["confidence"] = float(meta_node.text)
else:
node_dict[prop] = meta_node.text
def parse(self, values_are_confidence=False, rooted=False):
"""Parse the text stream this object was initialized with."""
nexml_doc = ElementTree.iterparse(self.handle, events=("end",))
for event, node in nexml_doc:
if node.tag == qUri("nex:tree"):
node_dict = {}
node_children = {}
root = None
nodes = []
edges = []
for child in node:
if child.tag == qUri("nex:node"):
nodes.append(child)
if child.tag == qUri("nex:edge"):
edges.append(child)
for node in nodes:
node_id = node.attrib["id"]
this_node = node_dict[node_id] = {}
if "otu" in node.attrib and node.attrib["otu"]:
this_node["name"] = node.attrib["otu"]
if "root" in node.attrib and node.attrib["root"] == "true":
root = node_id
for child in node:
if child.tag == qUri("nex:meta"):
self.add_annotation(node_dict[node_id], child)
srcs = set()
tars = set()
for edge in edges:
src, tar = edge.attrib["source"], edge.attrib["target"]
srcs.add(src)
tars.add(tar)
if src not in node_children:
node_children[src] = set()
node_children[src].add(tar)
if "length" in edge.attrib:
node_dict[tar]["branch_length"] = float(edge.attrib["length"])
if "property" in edge.attrib and edge.attrib["property"] in matches(
"cdao:has_Support_Value"
):
node_dict[tar]["confidence"] = float(edge.attrib["content"])
for child in edge:
if child.tag == qUri("nex:meta"):
self.add_annotation(node_dict[tar], child)
if root is None:
# if no root specified, start the recursive tree creation function
# with the first node that's not a child of any other nodes
rooted = False
possible_roots = (
node.attrib["id"]
for node in nodes
if node.attrib["id"] in srcs and node.attrib["id"] not in tars
)
root = next(possible_roots)
else:
rooted = True
yield NeXML.Tree(
root=self._make_tree(root, node_dict, node_children), rooted=rooted
)
@classmethod
def _make_tree(cls, node, node_dict, children):
"""Traverse the tree creating a nested clade structure (PRIVATE).
Return a NeXML.Clade, and calls itself recursively for each child,
traversing the entire tree and creating a nested structure of NeXML.Clade
objects.
"""
this_node = node_dict[node]
clade = NeXML.Clade(**this_node)
if node in children:
clade.clades = [
cls._make_tree(child, node_dict, children) for child in children[node]
]
return clade
# ---------------------------------------------------------
# Output
class Writer:
"""Based on the writer in Bio.Nexus.Trees (str, to_string)."""
def __init__(self, trees):
"""Initialize parameters for NeXML writer."""
self.trees = trees
self.node_counter = 0
self.edge_counter = 0
self.tree_counter = 0
def new_label(self, obj_type):
"""Create new labels for the NeXML writer."""
counter = f"{obj_type}_counter"
setattr(self, counter, getattr(self, counter) + 1)
return f"{obj_type}{getattr(self, counter)}"
def write(self, handle, cdao_to_obo=True, **kwargs):
"""Write this instance's trees to a file handle."""
self.cdao_to_obo = cdao_to_obo
# set XML namespaces
root_node = ElementTree.Element("nex:nexml")
root_node.set("version", VERSION)
root_node.set("xmlns", DEFAULT_NAMESPACE)
root_node.set("xsi:schemaLocation", SCHEMA)
for prefix, uri in NAMESPACES.items():
root_node.set(f"xmlns:{prefix}", uri)
otus = ElementTree.SubElement(
root_node, "otus", **{"id": "tax", "label": "RootTaxaBlock"}
)
# create trees
trees = ElementTree.SubElement(
root_node,
"trees",
**{"id": "Trees", "label": "TreesBlockFromXML", "otus": "tax"},
)
count = 0
tus = set()
for tree in self.trees:
this_tree = ElementTree.SubElement(
trees, "tree", **{"id": self.new_label("tree")}
)
first_clade = tree.clade
tus.update(self._write_tree(first_clade, this_tree, rooted=tree.rooted))
count += 1
# create OTUs
for tu in tus:
otu = ElementTree.SubElement(otus, "otu", **{"id": tu})
# write XML document to file handle
# xml_doc = ElementTree.ElementTree(root_node)
# xml_doc.write(handle,
# xml_declaration=True, encoding='utf-8',
# method='xml')
# use xml.dom.minodom for pretty printing
rough_string = ElementTree.tostring(root_node, "utf-8")
reparsed = minidom.parseString(rough_string)
try:
# XML handles ought to be in binary mode
handle.write(reparsed.toprettyxml(indent=" ").encode("utf8"))
except TypeError:
# Fall back for text mode
handle.write(reparsed.toprettyxml(indent=" "))
return count
def _write_tree(self, clade, tree, parent=None, rooted=False):
"""Recursively process tree, adding nodes and edges to Tree object (PRIVATE).
Returns a set of all OTUs encountered.
"""
tus = set()
convert_uri = cdao_to_obo if self.cdao_to_obo else (lambda s: s)
node_id = self.new_label("node")
clade.node_id = node_id
attrib = {"id": node_id, "label": node_id}
root = rooted and parent is None
if root:
attrib["root"] = "true"
if clade.name:
tus.add(clade.name)
attrib["otu"] = clade.name
node = ElementTree.SubElement(tree, "node", **attrib)
if parent is not None:
edge_id = self.new_label("edge")
attrib = {
"id": edge_id,
"source": parent.node_id,
"target": node_id,
"length": str(clade.branch_length),
"typeof": convert_uri("cdao:Edge"),
}
try:
confidence = clade.confidence
except AttributeError:
pass
else:
if confidence is not None:
attrib.update(
{
"property": convert_uri("cdao:has_Support_Value"),
"datatype": "xsd:float",
"content": f"{confidence:1.2f}",
}
)
node = ElementTree.SubElement(tree, "edge", **attrib)
if not clade.is_terminal():
for new_clade in clade.clades:
tus.update(self._write_tree(new_clade, tree, parent=clade))
del clade.node_id
return tus
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