def read(self):
"""
Returns gene annotation list and ontology graph read from nexo file.
"""
content_handler = NexoContentHandler(self.get_all_attrs, self.annotation_source)
xml.sax.parse(self.handle, content_handler)
annotations = []
for obj, assocs in content_handler.annotations.items():
annotations.append(GeneAnnotation(obj,
associations = [TermAssociation(x) for x in assocs]))
graph = OntologyGraph()
for _, node in content_handler.nodes.items():
graph.add_node(node.id, node)
edge_types = set()
for edge in content_handler.edges:
source = content_handler.nodes[edge[0]].id
target = content_handler.nodes[edge[1]].id
graph.add_edge(target, source, edge[2]) # in our representation it is inverted
edge_types.add(edge[2])
for edge_type in edge_types:
graph.typedefs[edge_type] = {"id" : edge_type}
return (annotations, graph)
def terms_to_graph(terms):
"""
Crates OntologyGraph from terms list obtained from OboIterator
"""
g = OntologyGraph()
defined_relations = set()
found_relations = set()
for (term_type, data) in terms:
if term_type == "Term": # Add only terms and typedefs for now
nid = data.pop("id")[0]
name = data.pop("name")[0]
term = OntologyTerm(nid, name, data)
if g.node_exists(nid):
g.update_node(nid, term)
else:
g.add_node(nid, term)
if "is_a" in data:
for edge in data["is_a"]:
g.add_edge(nid, edge, "is_a")
if "synonym" in data:
node = g.get_node(nid)
for synonym in data["synonym"]:
g.synonyms[shlex.split(synonym)[0]] = node
if "relationship" in data:
for edge in data["relationship"]:
p = edge.split()
if len(p) == 2:
g.add_edge(nid, p[1], p[0])
found_relations.add(p[0])
else:
raise ValueError("Incorrect relationship: " + edge)
if "alt_id" in data:
for alt_id in data["alt_id"]:
g.alt_ids[alt_id] = nid
if "namespace" in data:
g.namespace[nid] = data.pop("namespace")[0]
elif term_type == "Typedef":
rid = data["id"][0]
g.typedefs[rid] = data
defined_relations.add(rid)
# validate whether all relationships were defined
not_defined = found_relations.difference(defined_relations)
if len(not_defined) > 0:
raise ValueError("Undefined relationships found: " + str(not_defined))
g.typedefs["is_a"] = _IS_A_TYPE
for alt_id in g.alt_ids:
g.namespace[alt_id] = g.namespace[g.alt_ids[alt_id]]
return g
def terms_to_graph(terms):
"""
Crates OntologyGraph from terms list obtained from OboIterator
"""
g = OntologyGraph()
defined_relations = set()
found_relations = set()
for (term_type, data) in terms:
if term_type == "Term": # Add only terms and typedefs for now
nid = data.pop("id")[0]
name = data.pop("name")[0]
term = OntologyTerm(nid, name, data)
if g.node_exists(nid):
g.update_node(nid, term)
else:
g.add_node(nid, term)
if "is_a" in data:
for edge in data["is_a"]:
g.add_edge(nid, edge, "is_a")
if "synonym" in data:
node = g.get_node(nid)
for synonym in data["synonym"]:
g.synonyms[shlex.split(synonym)[0]] = node
if "relationship" in data:
for edge in data["relationship"]:
p = edge.split()
if len(p) == 2:
g.add_edge(nid, p[1], p[0])
found_relations.add(p[0])
else:
raise ValueError("Incorrect relationship: " + edge)
if "alt_id" in data:
for alt_id in data["alt_id"]:
g.alt_ids[alt_id] = nid
if "namespace" in data:
g.namespace[nid] = data.pop("namespace")[0]
elif term_type == "Typedef":
rid = data["id"][0]
g.typedefs[rid] = data
defined_relations.add(rid)
# validate whether all relationships were defined
not_defined = found_relations.difference(defined_relations)
if len(not_defined) > 0:
raise ValueError("Undefined relationships found: " + str(not_defined))
g.typedefs["is_a"] = _IS_A_TYPE
for alt_id in g.alt_ids:
g.namespace[alt_id] = g.namespace[g.alt_ids[alt_id]]
return g
