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 _init_dcnt(self):
"""Initialize descendant count."""
id2descendants = get_id2children(self.name2obj.values())
for id_, descendants in id2descendants.items():
obj = self.name2obj[id_]
obj.descendants = descendants
obj.dcnt = len(descendants)
def __init__(self, go2obj, relationships, dcnt, go2letter):
# Subset go2obj contains only items needed by go_sources
self.go2obj = go2obj
self.relationships = relationships
self.dcnt = dcnt
self.go2letter = go2letter
# Ex: set(['part_of', 'regulates', 'negatively_regulates', 'positively_regulates'])
_goobjs, _altgo2goobj = get_goobjs_altgo2goobj(self.go2obj)
_r0 = not relationships # True if not using relationships
self.go2descendants = get_id2children(
_goobjs) if _r0 else get_id2lower(_goobjs)
self.go2parents = get_id2parents(_goobjs) if _r0 else get_id2upper(
_goobjs)
self.go2dcnt = {go: len(p) for go, p in self.go2descendants.items()}
add_alt_goids(self.go2parents, _altgo2goobj)
add_alt_goids(self.go2descendants, _altgo2goobj)
add_alt_goids(self.go2dcnt, _altgo2goobj)
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 = {}
for goobj in go2obj.values():
go2children_orig[goobj.id] = goobj.get_all_children()
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_go3children", prt)
# Compare children lists
_chk_a2bset(go2children_orig, go2children_fast)
def get_go2children_go2obj(go2obj):
"""Return go2children (set of child GO IDs) for all GO ID keys in go2obj."""
goobjs, altgo2goobj = get_goobjs_altgo2goobj(go2obj)
go2children = get_id2children(goobjs)
add_alt_goids(go2children, altgo2goobj)
return go2children
def get_go2children_go2obj(go2obj):
"""Return go2children (set of child GO IDs) for all GO ID keys in go2obj."""
goobjs, altgo2goobj = get_goobjs_altgo2goobj(go2obj)
go2children = get_id2children(goobjs)
add_alt_goids(go2children, altgo2goobj)
return go2children