def main(args):
print args
# dump ttd targets and drugs:
ttd_targets=Target.objects.filter(src='ttd')
print 'ttd: %d targets' % len(ttd_targets)
# dump drugbank targets
db_targets=Target.objects.filter(src='db')
print 'db: %d targets\n' % len(db_targets)
# list shared targets in various ways
shared('name')
shared('gene_sym')
shared('uniprot_id')
# Look up Sam genes:
genelist=readgenes(args.samgenes_fn)
SamGenesWithUniprot(genelist, uniprot2gene(args.uniprot_gene_fn))
SamGenes(genelist)
# Look up tripNeg genes:
genelist=readgenes(args.tripnegs_fn)
g2s=gene2synonyms(args.gene2syn_fn)
tripNegAll(genelist, g2s)
def __init__(self, **kwargs):
self.cur_obj=None
self.cur_drug=None
self.cur_target=None
self.attr_name=None
# clear tables if called for:
if 'clear_table' in kwargs and kwargs['clear_table']:
print 'clearing tables...'
for cls in [ Drug, DrugSynonym, DrugPathway, Target, TargetSynonym, TargetPathway]:
dao=dao_django(cls=cls)
query = {'src':'db'} if cls==Drug or cls==Target else {}
dao.remove(query)
self.stats={'n_drugs':0,
'n_targets':0,
'n_drug_syns':0,
'n_target_syns':0,
'n_drug_pathways':0,
'n_target_pathways':0,
}
self.ug=uniprot2gene(kwargs['uniprot_gene_fn'])
def __init__(self, **kwargs):
self.db_name=kwargs['db']
self.cur_target=None
self.cur_id=None
self.targets=[]
# fixme: all of this should really be in the dao_django class
if 'clear_table' in kwargs and kwargs['clear_table']:
print 'clearing tables...'
for cls in [ Drug, DrugSynonym, DrugPathway, Target, TargetSynonym, TargetPathway]:
objs=cls.objects.all()
try:
objs.delete()
except django.db.utils.DatabaseError:
print 'clearing objects the long way for %s' % cls.__name__
for o in objs:
o.delete()
self.stats={'n_drugs':0,
'n_targets':0,
'n_pathways':0}
self.ug=uniprot2gene(kwargs['uniprot_gene_fn'])