def _init_go2dag(self, goids):
"""Get all GO IDs in the DAG above and including GO IDs in goids arg"""
# GO terms provided by user
##tic = timeit.default_timer()
s_godag = self.godag
rels = self.rels
go_set_all = set(goids)
go_set_cur = go_set_all.intersection(s_godag.keys())
if go_set_cur != go_set_all:
self._go_not_found(go_set_cur, go_set_all)
# Ancestor GO terms for each user GO term
##tic = prt_hms(tic, '_init_go2dag GO IDs not found')
go2ancestors = get_go2ancestors(self._get_goobjs(go_set_cur), rels)
##tic = prt_hms(tic, '_init_go2dag go2ancestors')
go2depth = self._get_go2depth(go2ancestors, rels)
##tic = prt_hms(tic, '_init_go2dag go2depth')
w_e = self.w_e
# pylint: disable=line-too-long
go2dag = {
go: DagA(go, ancestors, go2depth, w_e, s_godag)
for go, ancestors in go2ancestors.items()
}
##tic = prt_hms(tic, '_init_go2dag DagA')
# Add alt GO IDs
for go_alt in go_set_cur.difference(go2ancestors.keys()):
go_term = s_godag[go_alt]
go_main = go_term.item_id
go_depth = go_term.depth
if go_depth != 0:
go2dag[go_alt] = go2dag[go_main]
elif go_depth == 0:
go2dag[go_alt] = DagA(go_main, {}, go2depth, w_e, s_godag)
##tic = prt_hms(tic, '_init_go2dag ALT GO IDs')
return go2dag
def get_go_lineage_of(self, terms):
g = [self.GODAG[i] for i in terms]
g = get_go2ancestors(g, False)
gos = []
for key in g:
gos.append(key)
gos.extend(g[key])
return list(set(gos))
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_go2descendants(_goobjs, relationships)
self.go2ancestors = get_go2ancestors(_goobjs, relationships)
self.go2dcnt = cx.Counter({go: len(p) for go, p in self.go2descendants.items()})
add_alt_goids(self.go2ancestors, _altgo2goobj)
add_alt_goids(self.go2descendants, _altgo2goobj)
add_alt_goids(self.go2dcnt, _altgo2goobj)
def _init_go2genes(self, relationship_set, godag):
'''
Fills in the genes annotated to each GO, including ancestors
Due to the ontology structure, gene products annotated to
a GO Terma are also annotated to all ancestors.
'''
go2geneset = defaultdict(set)
go2up = get_go2ancestors(set(godag.values()), relationship_set)
# Fill go-geneset dict with GO IDs in annotations and their corresponding counts
for geneid, goids_anno in self.annots.items():
# Make a union of all the terms for a gene, if term parents are
# propagated but they won't get double-counted for the gene
allterms = set()
for goid_main in goids_anno:
allterms.add(goid_main)
if goid_main in go2up:
allterms.update(go2up[goid_main])
# Add 1 for each GO annotated to this gene product
for ancestor in allterms:
go2geneset[ancestor].add(geneid)
return dict(go2geneset)
def _init_go2genes(self, annots, relationships=None):
'''
Fills in the genes annotated to each GO, including ancestors
Due to the ontology structure, gene products annotated to
a GO Terma are also annotated to all ancestors.
'''
go2geneset = defaultdict(set)
if relationships is None:
relationships = {}
go2up = get_go2ancestors(set(self.go2obj.values()), relationships)
godag = self.go2obj
go_alts = set() # For alternate GO IDs
goids_notfound = set() # For missing GO IDs
# Fill go2geneset with GO IDs in annotations and their corresponding counts
for geneid, goids_anno in annots.items():
# Make a union of all the terms for a gene, if term parents are
# propagated but they won't get double-counted for the gene
allterms = set()
for goid_anno in goids_anno:
if goid_anno in godag:
goid_main = godag[goid_anno].item_id
if goid_anno != goid_main:
go_alts.add(goid_anno)
allterms.add(goid_main)
if goid_main in go2up:
allterms |= go2up[goid_main]
else:
goids_notfound.add(goid_anno)
# Add 1 for each GO annotated to this gene product
for ancestor in allterms:
go2geneset[ancestor].add(geneid)
if goids_notfound:
print("{N} Assc. GO IDs not found in the GODag\n".format(
N=len(goids_notfound)))
return dict(go2geneset), go_alts
def get_go2parents_go2obj(go2obj, relationships=None, prt=None):
"""Return go2parents (set of parent GO IDs) for all GO ID keys in go2obj."""
goobjs, altgo2goobj = get_goobjs_altgo2goobj(go2obj)
go2parents = get_go2ancestors(goobjs, relationships, prt)
add_alt_goids(go2parents, altgo2goobj)
return go2parents