def load_latest_go():
global go_updated
go_fname = go_client.go_owl_path
if not go_updated:
url = 'http://purl.obolibrary.org/obo/go.owl'
print("Downloading latest GO from %s" % url)
save_from_http(url, go_fname)
go_updated = True
return go_client.load_go_graph(go_fname)
def load_latest_go():
global go_updated
go_fname = go_client.go_owl_path
if not go_updated:
url = 'http://purl.obolibrary.org/obo/go.owl'
print("Downloading latest GO from %s" % url)
save_from_http(url, go_fname)
go_updated = True
return go_client.load_go_graph(go_fname)
g_bytes = g_bytes.replace(b'\n\n', b'\n').strip()
# Split into rows and sort
rows = g_bytes.split(b'\n')
rows.sort()
g_bytes = b'\n'.join(rows)
out_file.write(g_bytes)
def make_component_hierarchy(component_map, component_part_map):
g = rdflib.Graph()
indra_ns = 'http://sorger.med.harvard.edu/indra/'
ln = Namespace(indra_ns + 'locations/')
rn = Namespace(indra_ns + 'relations/')
part_of = rn.term('partof')
has_name = rn.term('hasName')
for comp_id, comp_name in component_map.items():
g.add((ln.term(comp_id), has_name, Literal(comp_name)))
sups = component_part_map.get(comp_id)
if sups is not None:
for sup_id in sups:
g.add((ln.term(comp_id), part_of, ln.term(sup_id)))
return g
if __name__ == '__main__':
g = go_client.load_go_graph()
component_map, component_part_map = go_client.get_cellular_components(g)
gg = make_component_hierarchy(component_map, component_part_map)
save_hierarchy(gg, rdf_file)
# Replace extra new lines in string and get rid of empty line at end
g_bytes = g_bytes.replace(b'\n\n', b'\n').strip()
# Split into rows and sort
rows = g_bytes.split(b'\n')
rows.sort()
g_bytes = b'\n'.join(rows)
out_file.write(g_bytes)
def make_component_hierarchy(component_map, component_part_map):
g = rdflib.Graph()
indra_ns = 'http://sorger.med.harvard.edu/indra/'
ln = Namespace(indra_ns + 'locations/')
rn = Namespace(indra_ns + 'relations/')
part_of = rn.term('partof')
has_name = rn.term('hasName')
for comp_id, comp_name in component_map.items():
g.add((ln.term(comp_id), has_name, Literal(comp_name)))
sups = component_part_map.get(comp_id)
if sups is not None:
for sup_id in sups:
g.add((ln.term(comp_id), part_of, ln.term(sup_id)))
return g
if __name__ == '__main__':
g = go_client.load_go_graph()
component_map, component_part_map = go_client.get_cellular_components(g)
gg = make_component_hierarchy(component_map, component_part_map)
save_hierarchy(gg, rdf_file)