def get(self): """ Returns homology associations for a given input set of genes """ args = parser.parse_args() M = GolrFields() rel = 'RO:0002434' # TODO; allow other types results = search_associations( subjects=args.get('subject'), select_fields=[M.SUBJECT, M.RELATION, M.OBJECT], use_compact_associations=True, relation=rel, rows=MAX_ROWS, facet_fields=[], **args) return results
def get(self): """ Summary statistics for objects associated """ args = parser.parse_args() M = GolrFields() results = search_associations( subjects=args.get('subject'), rows=0, facet_fields=[M.OBJECT_CLOSURE, M.IS_DEFINED_BY], facet_limit=-1, **args) print("RESULTS=" + str(results)) obj_count_dict = results['facet_counts'][M.OBJECT_CLOSURE] del results['facet_counts'][M.OBJECT_CLOSURE] return {'results': obj_count_dict, 'facets': results['facet_counts']}
def get(self): """ Returns compact associations for a given input set """ args = parser.parse_args() M = GolrFields() #results = search_associations(subjects=args.get('subject'), # rows=0, # pivot_subject_object=True, # facet_fields=[], # facet_limit=-1, # **args) results = search_associations( subjects=args.get('subject'), select_fields=[M.SUBJECT, M.RELATION, M.OBJECT], use_compact_associations=True, rows=MAX_ROWS, facet_fields=[], **args) return results
""" Quick similarity calculations """ from biogolr.golr_associations import search_associations, GolrFields import scipy.stats # TODO - move import scipy as sp # TODO - move M = GolrFields() def get_object_closure(subject, object_category=None, **kwargs): """ Find all terms used to annotate subject plus ancestors """ results = search_associations(subject=subject, object_category=object_category, select_fields=[], facet_fields=[M.OBJECT_CLOSURE], facet_limit=-1, rows=0, **kwargs) return set(results['facet_counts'][M.OBJECT_CLOSURE].keys()) def subject_pair_overlap(subject1, subject2, object_category=None, **kwargs): """ Jaccard similarity """