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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 RDF/CDAO file format.
This is an RDF format that conforms to the Comparative Data Analysis Ontology (CDAO).
See: http://evolutionaryontology.org/cdao
This module requires the librdf Python bindings (http://www.librdf.org)
The CDAOIO.Parser, in addition to parsing text files, can also parse directly
from a triple store that implements the Redland storage interface; similarly,
the CDAOIO.Writer can store triples in a triple store instead of serializing
them to a file.
"""
import os
from io import StringIO
from Bio import MissingPythonDependencyError
from Bio.Phylo import CDAO
from ._cdao_owl import cdao_namespaces, resolve_uri
# import of cdao_elements from ._cdao_owl removed in Biopython 1.74
try:
import rdflib
rdfver = rdflib.__version__
if rdfver[0] in ["1", "2"] or (rdfver in ["3.0.0", "3.1.0", "3.2.0"]):
raise MissingPythonDependencyError(
"Support for CDAO tree format requires RDFlib v3.2.1 or later."
)
except ImportError:
raise MissingPythonDependencyError(
"Support for CDAO tree format requires RDFlib."
) from None
RDF_NAMESPACES = {
"owl": "http://www.w3.org/2002/07/owl#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
}
RDF_NAMESPACES.update(cdao_namespaces)
# pad node ids with zeroes until they're at least this length
ZEROES = 8
def qUri(x):
"""Resolve URI for librdf."""
return resolve_uri(x, namespaces=RDF_NAMESPACES)
def format_label(x):
"""Format label for librdf."""
return x.replace("_", " ")
# ---------------------------------------------------------
# Public API
def parse(handle, **kwargs):
"""Iterate over the trees in a CDAO file handle.
:returns: generator of Bio.Phylo.CDAO.Tree objects.
"""
return Parser(handle).parse(**kwargs)
def write(trees, handle, plain=False, **kwargs):
"""Write a trees in CDAO format to the given file handle.
:returns: number of trees written.
"""
return Writer(trees).write(handle, plain=plain, **kwargs)
# ---------------------------------------------------------
# Input
class Parser:
"""Parse a CDAO tree given a file handle."""
def __init__(self, handle=None):
"""Initialize CDAO tree parser."""
self.handle = handle
self.graph = None
self.node_info = None
self.children = {}
self.rooted = False
@classmethod
def from_string(cls, treetext):
"""Instantiate the class from the given string."""
handle = StringIO(treetext)
return cls(handle)
def parse(self, **kwargs):
"""Parse the text stream this object was initialized with."""
self.parse_handle_to_graph(**kwargs)
return self.parse_graph()
def parse_handle_to_graph(
self, rooted=False, parse_format="turtle", context=None, **kwargs
):
"""Parse self.handle into RDF model self.model."""
if self.graph is None:
self.graph = rdflib.Graph()
graph = self.graph
for k, v in RDF_NAMESPACES.items():
graph.bind(k, v)
self.rooted = rooted
if "base_uri" in kwargs:
base_uri = kwargs["base_uri"]
else:
# Windows style slashes cannot be used in an RDF URI
base_uri = "file://" + os.path.abspath(self.handle.name).replace("\\", "/")
graph.parse(file=self.handle, publicID=base_uri, format=parse_format)
return self.parse_graph(graph, context=context)
def parse_graph(self, graph=None, context=None):
"""Iterate over RDF model yielding CDAO.Tree instances."""
if graph is None:
graph = self.graph
# look up branch lengths/TUs for all nodes
self.get_node_info(graph, context=context)
for root_node in self.tree_roots:
clade = self.parse_children(root_node)
yield CDAO.Tree(root=clade, rooted=self.rooted)
def new_clade(self, node):
"""Return a CDAO.Clade object for a given named node."""
result = self.node_info[node]
kwargs = {}
if "branch_length" in result:
kwargs["branch_length"] = result["branch_length"]
if "label" in result:
kwargs["name"] = result["label"].replace("_", " ")
if "confidence" in result:
kwargs["confidence"] = result["confidence"]
clade = CDAO.Clade(**kwargs)
return clade
def get_node_info(self, graph, context=None):
"""Create a dictionary containing information about all nodes in the tree."""
self.node_info = {}
self.obj_info = {}
self.children = {}
self.nodes = set()
self.tree_roots = set()
assignments = {
qUri("cdao:has_Parent"): "parent",
qUri("cdao:belongs_to_Edge_as_Child"): "edge",
qUri("cdao:has_Annotation"): "annotation",
qUri("cdao:has_Value"): "value",
qUri("cdao:represents_TU"): "tu",
qUri("rdfs:label"): "label",
qUri("cdao:has_Support_Value"): "confidence",
}
for s, v, o in graph:
# process each RDF triple in the graph sequentially
s, v, o = str(s), str(v), str(o)
if s not in self.obj_info:
self.obj_info[s] = {}
this = self.obj_info[s]
try:
# if the predicate is one we care about, store information for
# later
this[assignments[v]] = o
except KeyError:
pass
if v == qUri("rdf:type"):
if o in (qUri("cdao:AncestralNode"), qUri("cdao:TerminalNode")):
# this is a tree node; store it in set of all nodes
self.nodes.add(s)
if v == qUri("cdao:has_Root"):
# this is a tree; store its root in set of all tree roots
self.tree_roots.add(o)
for node in self.nodes:
# for each node, look up all information needed to create a
# CDAO.Clade
self.node_info[node] = {}
node_info = self.node_info[node]
obj = self.obj_info[node]
if "edge" in obj:
# if this object points to an edge, we need a branch length from
# the annotation on that edge
edge = self.obj_info[obj["edge"]]
if "annotation" in edge:
annotation = self.obj_info[edge["annotation"]]
if "value" in annotation:
node_info["branch_length"] = float(annotation["value"])
if "tu" in obj:
# if this object points to a TU, we need the label of that TU
tu = self.obj_info[obj["tu"]]
if "label" in tu:
node_info["label"] = tu["label"]
if "parent" in obj:
# store this node as a child of its parent, if it has one,
# so that the tree can be traversed from parent to children
parent = obj["parent"]
if parent not in self.children:
self.children[parent] = []
self.children[parent].append(node)
def parse_children(self, node):
"""Traverse the tree to create a nested clade structure.
Return a CDAO.Clade, and calls itself recursively for each child,
traversing the entire tree and creating a nested structure of CDAO.Clade
objects.
"""
clade = self.new_clade(node)
children = self.children[node] if node in self.children else []
clade.clades = [self.parse_children(child_node) for child_node in children]
return clade
# ---------------------------------------------------------
# Output
class Writer:
"""Based on the writer in Bio.Nexus.Trees (str, to_string)."""
prefixes = RDF_NAMESPACES
def __init__(self, trees):
"""Initialize parameters for writing a CDAO tree."""
self.trees = trees
self.node_counter = 0
self.edge_counter = 0
self.tu_counter = 0
self.tree_counter = 0
def write(
self,
handle,
tree_uri="",
record_complete_ancestry=False,
rooted=False,
**kwargs,
):
"""Write this instance's trees to a file handle."""
self.rooted = rooted
self.record_complete_ancestry = record_complete_ancestry
if tree_uri and not tree_uri.endswith("/"):
tree_uri += "/"
trees = self.trees
if tree_uri:
handle.write(f"@base <{tree_uri}>\n")
for k, v in self.prefixes.items():
handle.write(f"@prefix {k}: <{v}> .\n")
handle.write(f"<{self.prefixes['cdao']}> a owl:Ontology .\n")
for tree in trees:
self.tree_counter += 1
self.tree_uri = "tree%s"
first_clade = tree.clade
statements = self.process_clade(first_clade, root=tree)
for stmt in statements:
self.add_stmt_to_handle(handle, stmt)
def add_stmt_to_handle(self, handle, stmt):
"""Add URI prefix to handle."""
# apply URI prefixes
stmt_strings = []
for n, part in enumerate(stmt):
if isinstance(part, rdflib.URIRef):
node_uri = str(part)
changed = False
for prefix, uri in self.prefixes.items():
if node_uri.startswith(uri):
node_uri = node_uri.replace(uri, f"{prefix}:", 1)
if node_uri == "rdf:type":
node_uri = "a"
changed = True
if changed or ":" in node_uri:
stmt_strings.append(node_uri)
else:
stmt_strings.append(f"<{node_uri}>")
elif isinstance(part, rdflib.Literal):
stmt_strings.append(part.n3())
else:
stmt_strings.append(str(part))
handle.write(f"{' '.join(stmt_strings)} .\n")
def process_clade(self, clade, parent=None, root=False):
"""Recursively generate triples describing a tree of clades."""
self.node_counter += 1
clade.uri = f"node{str(self.node_counter).zfill(ZEROES)}"
if parent:
clade.ancestors = parent.ancestors + [parent.uri]
else:
clade.ancestors = []
def nUri(s):
# nUri = lambda s: rdflib.URIRef(s)
return rdflib.URIRef(s)
def pUri(s):
# pUri = lambda s: rdflib.URIRef(qUri(s))
return rdflib.URIRef(qUri(s))
tree_id = nUri("")
statements = []
if root is not False:
# create a cdao:RootedTree with reference to the tree root
tree_type = (
pUri("cdao:RootedTree") if self.rooted else pUri("cdao:UnrootedTree")
)
statements += [
(tree_id, pUri("rdf:type"), tree_type),
(tree_id, pUri("cdao:has_Root"), nUri(clade.uri)),
]
try:
tree_attributes = root.attributes
except AttributeError:
tree_attributes = []
for predicate, obj in tree_attributes:
statements.append((tree_id, predicate, obj))
if clade.name:
# create TU
self.tu_counter += 1
tu_uri = f"tu{str(self.tu_counter).zfill(ZEROES)}"
statements += [
(nUri(tu_uri), pUri("rdf:type"), pUri("cdao:TU")),
(nUri(clade.uri), pUri("cdao:represents_TU"), nUri(tu_uri)),
(
nUri(tu_uri),
pUri("rdfs:label"),
rdflib.Literal(format_label(clade.name)),
),
]
try:
tu_attributes = clade.tu_attributes
except AttributeError:
tu_attributes = []
for predicate, obj in tu_attributes:
yield (nUri(tu_uri), predicate, obj)
# create this node
node_type = "cdao:TerminalNode" if clade.is_terminal() else "cdao:AncestralNode"
statements += [
(nUri(clade.uri), pUri("rdf:type"), pUri(node_type)),
(nUri(clade.uri), pUri("cdao:belongs_to_Tree"), tree_id),
]
if parent is not None:
# create edge from the parent node to this node
self.edge_counter += 1
edge_uri = f"edge{str(self.edge_counter).zfill(ZEROES)}"
statements += [
(nUri(edge_uri), pUri("rdf:type"), pUri("cdao:DirectedEdge")),
(nUri(edge_uri), pUri("cdao:belongs_to_Tree"), tree_id),
(nUri(edge_uri), pUri("cdao:has_Parent_Node"), nUri(parent.uri)),
(nUri(edge_uri), pUri("cdao:has_Child_Node"), nUri(clade.uri)),
(
nUri(clade.uri),
pUri("cdao:belongs_to_Edge_as_Child"),
nUri(edge_uri),
),
(nUri(clade.uri), pUri("cdao:has_Parent"), nUri(parent.uri)),
(
nUri(parent.uri),
pUri("cdao:belongs_to_Edge_as_Parent"),
nUri(edge_uri),
),
]
try:
confidence = clade.confidence
except AttributeError:
pass
else:
if confidence is not None:
confidence = rdflib.Literal(
confidence, datatype="http://www.w3.org/2001/XMLSchema#decimal"
)
statements += [
(nUri(clade.uri), pUri("cdao:has_Support_Value"), confidence)
]
if self.record_complete_ancestry and len(clade.ancestors) > 0:
statements += [
(nUri(clade.uri), pUri("cdao:has_Ancestor"), nUri(ancestor))
for ancestor in clade.ancestors
]
if clade.branch_length is not None:
# add branch length
edge_ann_uri = f"edge_annotation{str(self.edge_counter).zfill(ZEROES)}"
branch_length = rdflib.Literal(
clade.branch_length,
datatype=rdflib.URIRef("http://www.w3.org/2001/XMLSchema#decimal"),
)
statements += [
(nUri(edge_ann_uri), pUri("rdf:type"), pUri("cdao:EdgeLength")),
(nUri(edge_uri), pUri("cdao:has_Annotation"), nUri(edge_ann_uri)),
(nUri(edge_ann_uri), pUri("cdao:has_Value"), branch_length),
]
try:
edge_attributes = clade.edge_attributes
except AttributeError:
edge_attributes = []
for predicate, obj in edge_attributes:
yield (nUri(edge_uri), predicate, obj)
yield from statements
try:
clade_attributes = clade.attributes
except AttributeError:
clade_attributes = []
for predicate, obj in clade_attributes:
yield (nUri(clade.uri), predicate, obj)
if not clade.is_terminal():
for new_clade in clade.clades:
yield from self.process_clade(new_clade, parent=clade, root=False)
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