def test_get_lowerselect(prt=sys.stdout):
"""Test getting parents and user-specfied ancestor relationships"""
# Load GO-DAG
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, 'go-basic.obo'), optional_attrs='relationship')
run = RelationshipCombos(godag)
run.chk_relationships_all()
rels_combo = run.get_relationship_combos()
print('{N} COMBINATIONS OF RELATIONSHIPS'.format(N=len(rels_combo)))
for relidx, rels_set in enumerate(rels_combo, 1):
print('{I}) RELATIONSHIPS[{N}]: {Rs}'.format(
I=relidx, N=len(rels_set), Rs=' '.join(sorted(rels_set))))
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using get_all_parents in GOTerm class
tic = timeit.default_timer()
# pylint: disable=line-too-long
go2lowerselect_orig = {o.item_id:get_all_lowerselect(o, rels_set) for o in run.go2obj.values()}
tic = prt_hms(tic, "Get all goobj's parents using get_all_lowerselect(GOTerm)", prt)
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using GOTerm get_all_parents
go2lowerselect_fast = get_id2lowerselect(run.go2obj.values(), rels_set)
tic = prt_hms(tic, "Get all goobj's parents using go_tasks::get_id2lowerselect", prt)
# ------------------------------------------------------------------------
# Compare parent lists
chkr = CheckGOs('test_get_lower_select', godag)
chkr.chk_a2bset(go2lowerselect_orig, go2lowerselect_fast) # EXPECTED, ACTUAL
print("PASSED: get_lowerselect RELATIONSHIPS[{N}]: {Rs}".format(
N=len(rels_set), Rs=' '.join(sorted(rels_set))))
def test_get_children(prt=sys.stdout):
"""Semantic Similarity test for Issue #86."""
# Load GO-DAG
fin_obo = "go-basic.obo"
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, fin_obo))
go2obj = {go: o for go, o in godag.items() if go == o.id}
# Get all children for all GO IDs using get_all_children in GOTerm class
tic = timeit.default_timer()
go2children_orig = {}
go2children_empty = set()
for goobj in go2obj.values():
children = goobj.get_all_children()
if children:
go2children_orig[goobj.id] = children
else:
go2children_empty.add(goobj.id)
tic = prt_hms(tic,
"Get all goobj's children using GOTerm.get_all_children()",
prt)
# Get all children for all GO IDs using GOTerm get_all_children
go2children_fast = get_id2children(go2obj.values())
prt_hms(tic, "Get all goobj's children using go_tasks::get_id2children",
prt)
# Compare children lists
CheckGOs('test_get_children', go2obj).chk_a2bset(go2children_orig,
go2children_fast)
def test_get_parent(prt=sys.stdout):
"""Semantic Similarity test for Issue #86."""
# Load GO-DAG
fin_obo = "go-basic.obo"
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, fin_obo))
go2obj = {go: o for go, o in godag.items() if go == o.id}
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using get_all_parents in GOTerm class
tic = timeit.default_timer()
go2parents_orig = {}
## go_noparents = set()
for goterm in go2obj.values():
parents = goterm.get_all_parents()
#if parents:
go2parents_orig[goterm.id] = parents
#else:
# go_noparents.add(goterm.id)
tic = prt_hms(tic,
"Get all goobj's parents using GOTerm.get_all_parents()",
prt)
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using GOTerm get_all_parents
go2parents_fast = get_id2parents(go2obj.values())
tic = prt_hms(tic,
"Get all goobj's parents using go_tasks::get_id2parents",
prt)
# ------------------------------------------------------------------------
go2parents_fast2 = get_id2parents2(go2obj.values())
tic = prt_hms(tic,
"Get all goobj's parents using go_tasks::get_id2parents2",
prt)
# ------------------------------------------------------------------------
# Compare parent lists
chkr = CheckGOs('test_get_parents', go2obj)
chkr.chk_a2bset_equiv(go2parents_orig, go2parents_fast)
chkr.chk_a2bset_equiv(go2parents_orig, go2parents_fast2)
print("PASSED: get_parent test")