def test_remote_sparql():
"""
reconstitution test
"""
factory = OntologyFactory()
# default method is sparql
ont = factory.create('pato')
g = ont.get_graph()
info = g.node[PLOIDY]
print(str(info))
nodes = g.nodes()
print(len(nodes))
assert len(nodes) > 100
nbrs = g.successors(PLOIDY)
print("SUCC:" + str(nbrs))
parents = g.predecessors(PLOIDY)
print("PRED:" + str(parents))
assert parents == ['PATO:0001396']
ancs = ancestors(g, PLOIDY)
print("ANCS:" + str(ancs))
assert 'PATO:0000001' in ancs
print(g)
Q = ['.*shape.*']
w = GraphRenderer.create('tree')
shapes1 = ont.resolve_names(Q, is_regex=True, is_remote=False)
print("SHAPE Q:" + str(shapes1))
show_nodes(w, ont, shapes1)
assert Y_SHAPED in shapes1
shapes2 = ont.resolve_names(Q, is_regex=True, is_remote=True)
print("SHAPE Q:" + str(shapes2))
show_nodes(w, ont, shapes2)
assert Y_SHAPED in shapes2
def test_write():
"""
write obo from json
"""
factory = OntologyFactory()
print("Creating ont")
ont = factory.create('tests/resources/nucleus.json')
w = GraphRenderer.create('obo')
w.write(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 test_local_json_parse():
"""
Load ontology from JSON
"""
factory = OntologyFactory()
print("Creating ont")
#tbox_ontology = factory.create('go')
# TODO: create test module for this example
tbox_ontology = factory.create('tests/resources/go-truncated-pombase.json')
ont = factory.create('tests/resources/gocam-example.ttl', tbox_ontology=tbox_ontology)
g = ont.get_graph()
nodes = ont.search('%')
print("NODES: {}".format(nodes))
w = GraphRenderer.create(None)
w.write_subgraph(ont, nodes)
i = 'http://model.geneontology.org/0000000300000001/0000000300000007'
ni = g[i]
print(str(ni))
['GO:0060070'] == ni['types']
nbrs = ont.neighbors(i)
print("NEIGHBORS: {}".format(nbrs))
subont = tbox_ontology.subontology(nodes, minimal=False)
w = GraphRenderer.create('obo')
print(w.render(subont))
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)
def todo_subontology():
"""
subontology
"""
factory = OntologyFactory()
print("Creating ont")
ont = factory.create('scigraph:ontology')
print("ONT NODES: {}".format(ont.nodes()))
# TODO: implement this for SciGraph:
subont = ont.subontology(relations=['subClassOf'])
PERM = 'GO:1990578'
print("NODES: {}".format(subont.nodes()))
ancs = subont.ancestors(PERM, reflexive=True)
print(str(ancs))
for a in ancs:
print(" ANC: {} '{}'".format(a,subont.label(a)))
assert len(ancs) > 0
from ontobio.io.ontol_renderers import GraphRenderer
w = GraphRenderer.create('tree')
w.write_subgraph(ont, ancs)
def test_factory():
"""
test ontology factory using wikidata as source and using PTSD.
"""
f = OntologyFactory()
ont = f.create('wdq:Q544006')
for n in ont.nodes():
print('{} "{}"'.format(n, ont.label(n)))
qids = ont.search('anxiety%')
assert len(qids) > 0
print(qids)
nodes = ont.traverse_nodes(qids, up=True, down=True)
print(nodes)
assert len(nodes) > 0
labels = [ont.label(n) for n in nodes]
print(labels)
# Note: it's possible wd may change rendering this false
assert 'Fear of frogs' in labels
from ontobio.io.ontol_renderers import GraphRenderer
w = GraphRenderer.create('tree')
w.write(ont, query_ids=qids)
def extract_ontology(ont, aset, args):
ont = aset.subontology(minimal=args.minimal)
w = GraphRenderer.create('obo')
w.outfile = args.outfile
w.write(ont)
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
# Make ontology from wikidata
onto_factory = OntologyFactory()
wd_ontology = onto_factory.create('wdq:Q185034') # Sickle cell anemia
qids = wd_ontology.search('Sickle%')
# Traverse up and down from query node in our sub-ontology
nodes = wd_ontology.traverse_nodes(qids, up=True, down=True)
renderer = GraphRenderer.create('obo')
renderer.outfile = './output/wd-ontology.obo'
# renderer.write(wd_ontology)
# >> AttributeError: 'EagerWikidataOntology' object has no attribute 'all_logical_definitions'
renderer.write_subgraph(wd_ontology, nodes, query_ids=qids)
# Get GO terms
outfile = open('./output/go-terms.tsv', 'w')
[ptsd] = wd_ontology.search('Sickle Cell Anemia')
proteins = wd.canned_query('disease2protein', ptsd)
go = onto_factory.create('go')
afactory = AssociationSetFactory()
all_terms = []
term_to_ancestors = {}
for t in common_terms:
subont = ont.subontology(ont.ancestors(t), relations=RELATIONS)
term_to_ancestors[t] = subont.nodes(
) # Keep ancestor list in case we want to only include common ancestors
for n in subont.nodes():
if n not in all_terms:
all_terms.append(n)
print("Grabbed all ancestors")
if ONLY_SHARED_ANCESTORS:
shared_ancestors = []
for t in common_terms:
for anc in term_to_ancestors[t]:
## x-y term matrix checking for shared ancestors in multiple ancestor sets
for other_t in common_terms:
if other_t == t:
continue
else:
if anc in term_to_ancestors[other_t]:
shared_ancestors.append(anc)
all_terms = set(shared_ancestors + list(common_terms.keys()))
print("Filtered for shared ancestors only")
print("{} terms included in panther_slim".format(len(all_terms)))
hierarchy_ont = ont.subontology(all_terms, relations=RELATIONS)
# hierarchy_ont = fill_in_relations(hierarchy_ont, ont)
renderer = GraphRenderer.create("obo")
renderer.outfile = OUTFILE
renderer.write(hierarchy_ont)