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
"""