def _get_goids_all(self, go_sources):
"""Given GO ID sources and optionally the relationship attribute, return all GO IDs."""
go2obj_user = {}
objrel = CurNHigher(self.relationships, self.godag)
objrel.get_go2obj_cur_n_high(go2obj_user, go_sources)
goids = set(go2obj_user)
for goterm in go2obj_user.values():
if goterm.alt_ids:
goids.update(goterm.alt_ids)
return goids
def _get_goids_all(self, go_sources):
"""Given GO ID sources and optionally the relationship attribute, return all GO IDs."""
go2obj_user = {}
objrel = CurNHigher(self.relationships, self.godag)
objrel.get_id2obj_cur_n_high(go2obj_user, go_sources)
goids = set(go2obj_user)
for goterm in go2obj_user.values():
if goterm.alt_ids:
goids.update(goterm.alt_ids)
return goids
def _init_gos(self, go_sources_arg, relationships_arg):
"""Initialize GO sources."""
# No GO sources provided
if not go_sources_arg:
assert self.go2obj_orig, "go2obj MUST BE PRESENT IF go_sources IS NOT"
self.go_sources = set(self.go2obj_orig)
self.go2obj = self.go2obj_orig
sys.stdout.write("**NOTE: {N:,} SOURCE GO IDS\n".format(N=len(self.go_sources)))
return
# GO sources provided
go_sources = self._init_go_sources(go_sources_arg, self.go2obj_orig)
# Create new go2obj_user subset matching GO sources
# Fill with source and parent GO IDs and alternate GO IDs
go2obj_user = {}
objrel = CurNHigher(relationships_arg, self.go2obj_orig)
objrel.get_go2obj_cur_n_high(go2obj_user, go_sources)
# Add additional GOTerm information, if needed for user task
kws_gos = {k:v for k, v in self.kws.items() if k in self.kws_aux_gos}
if kws_gos:
self._add_goterms_kws(go2obj_user, kws_gos)
self.go_sources = go_sources
self.go2obj = go2obj_user