def main(args):
print args
dt_dao=dao_mongo(cls=Drugcard, db=args.db_name)
query={}
for k,v in grouper(2, args.query):
query[k]=v
print 'query: %s' % query
targets=dt_dao.find(query, collection=args.collection)
print '%s: %d results' % (query, len(targets))
for t in targets:
print t
def main(args):
print args
path=args.path
dt_dao=dao_mongo(cls=rdf.graph, db=args.db_name)
query={'pred':'Pathway', 'obj':path}
drugs=dt_dao.find(query, collection=args.collection)
for d in drugs:
query={'pred':'Drug(s)', 'sub':d.sub}
targets=dt_dao.find(query, collection=args.collection)
if len(targets)==0: continue
print d
s='' if len(targets)==1 else 's'
print '%d target%s for %s' % (len(targets), s, d.sub)
for t in targets:
print t
print
def main(args):
'''
Do a gene (syn) -> target lookup in the mongo collection 'graph'
'''
print args
g_syn=args.gene
dt_dao=dao_mongo(cls=rdf.graph, db=args.db_name)
query={'pred':'Synonyms', 'obj':g_syn}
drugs=dt_dao.find(query, collection=args.collection)
# print '%s: %d results' % (query, len(drugs))
for d in drugs:
print d
query={'pred':'Drug(s)', 'sub':d.sub}
# print query
targets=dt_dao.find(query, collection=args.collection)
print '%d targets for %s' % (len(targets), d.sub)
for t in targets:
print t
print
def main(args):
'''
print out stats for mongo db
'''
print args
dc_dao=dao_mongo(cls=Drugcard, db='nof1')
drug_histo=Histogram()
pw_histo=Histogram()
gene_histo=Histogram()
for dc in dc_dao.iter({'_cls':'drugcard.Drugcard'}):
# print 'dc %s' % dc.id
if not dc.Drug_Type:
continue
if not ('Approved' in dc.Drug_Type or 'Biotech' in dc.Drug_Type):
continue
try:
drug_histo.add(dc.Generic_Name[0])
except IndexError:
print "no Generic_Name for %s" % dc.id
for pw in dc.Pathways:
pw_histo.add(pw)
for target in dc.targets:
try:
for pw in target.Pathway:
pw_histo.add(pw)
except AttributeError, e:
print "no Pathway for pw id=%s" % target.ID
try:
for gene in target.Gene_Name:
gene_histo.add(gene)
except AttributeError, e:
print "no Gene_Name for pw id=%s" % target.ID
def setUp(self):
self.dc_dao=dao_mongo(cls=Drugcard, db='test_nof1')
self.dc_dao.remove()
