def annotate(graph, organism=9606, aspects=('C', 'F', 'P')):
"""
Adds Gene Ontology annotations to the nodes of a graph.
:param igraph.Graph graph:
Any ``igraph.Graph`` object with uniprot IDs
in its ``name`` vertex attribute.
"""
aspects = aspects if type(aspects) in {list, tuple} else (aspects, )
graph.vs['go'] = [{
'C': set(),
'F': set(),
'P': set()
} for _ in xrange(graph.vcount())]
terms, annot = dataio.go_annotations_goa(organism=organism)
prg = progress.Progress(graph.vcount(), 'Loading GO annotations', 9)
for v in graph.vs:
prg.step()
for asp in aspects:
if v['name'] in annot[asp]:
v['go'][asp] = annot[asp][v['name']]
prg.terminate()
def __init__(self, organism=9606, ontology=None):
"""
For one organism loads Gene Ontology annotations, in addition it
accepts or creates a ``GeneOntology`` object.
"""
self.ontology = ontology or GeneOntology()
annot = dataio.go_annotations_goa(organism=organism)
self.c = annot['C']
self.f = annot['F']
self.p = annot['P']
self._ancestors_annotate()
self._merge_annotations()
def __init__(
self,
organism=9606,
ontology=None,
pickle_file=None,
use_pickle_cache=True,
):
"""
For one organism loads Gene Ontology annotations, in addition it
accepts or creates a ``GeneOntology`` object.
"""
session_mod.Logger.__init__(self, name='go')
self.organism = organism
self._pickle_file = pickle_file
self._use_pickle_cache = use_pickle_cache
if self._pickle_cache_load_hook():
return
self.ontology = ontology or GeneOntology()
self._log('Populating Gene Ontology: '
'annotations for organism `%u`.' % organism)
annot = dataio.go_annotations_goa(organism=organism)
self.c = annot['C']
self.f = annot['F']
self.p = annot['P']
self._ancestors_annotate()
self._merge_annotations()
self._pickle_cache_save_hook()
def test_go_annotations_goa(self):
goa = dataio.go_annotations_goa()
assert 'GO:0043235' in goa['C']['P00533']