def subontology(self, nodes=None, minimal=False, relations=None):
"""
Return a new ontology that is an extract of this one
Arguments
---------
- nodes: list
list of node IDs to include in subontology. If None, all are used
- relations: list
list of relation IDs to include in subontology. If None, all are used
"""
g = None
if nodes is not None:
g = self.subgraph(nodes)
else:
g = self.get_graph()
if minimal:
from ontobio.slimmer import get_minimal_subgraph
g = get_minimal_subgraph(g, nodes)
ont = Ontology(graph=g,
xref_graph=self.xref_graph) # TODO - add metadata
if relations is not None:
g = ont.get_filtered_graph(relations)
ont = Ontology(graph=g, xref_graph=self.xref_graph)
return ont
def render(ont, query_ids, args):
"""
Writes or displays graph
"""
if args.slim.find('m') > -1:
logging.info("SLIMMING")
g = get_minimal_subgraph(g, query_ids)
w = GraphRenderer.create(args.to)
if args.outfile is not None:
w.outfile = args.outfile
w.write(ont,
query_ids=query_ids,
container_predicates=args.container_properties)
def show_graph(g, nodes, query_ids, args):
"""
Writes graph
"""
if args.graph.find('m') > -1:
logging.info("SLIMMING")
g = get_minimal_subgraph(g, query_ids)
w = GraphRenderer.create(args.to)
if args.outfile is not None:
w.outfile = args.outfile
logging.info("Writing subg from " + str(g))
w.write(g,
query_ids=query_ids,
container_predicates=args.container_properties)
def render(ont, query_ids, args):
"""
Writes or displays graph
"""
if args.slim.find('m') > -1:
logging.info("SLIMMING")
g = get_minimal_subgraph(g, query_ids)
w = GraphRenderer.create(args.to)
if args.showdefs:
w.config.show_text_definition = True
if args.render:
if 'd' in args.render:
logging.info("Showing text defs")
w.config.show_text_definition = True
if args.outfile is not None:
w.outfile = args.outfile
w.write(ont,
query_ids=query_ids,
container_predicates=args.container_properties)