def main(args):
print args
# clear dbs:
if False:
dao_og=dao_django(cls=OncotatorGene)
dao_og.remove({})
dao_op=dao_django(cls=UniprotProtein)
dao_op.remove({})
genes=readgenes(args.in_fn)
base_url=args.base_url
stats={'n_genes':0, 'n_prots':0}
for gn in genes:
try:
gene=OncotatorGene.objects.get(name=gn)
print '%s: already loaded' % gn
continue
except OncotatorGene.DoesNotExist:
pass
url=base_url+gn
res=requests.get(url)
if res.status_code != 200:
print '%s: error/nothing found' % gn
continue
print gn
dct=json.loads(res.content)
# for k,v in dct.items():
# print '%s: %s' % (k,v)
gene=OncotatorGene(name=gn,
full_name=dct['full_name'],
chr=dct['chr'],
location=dct['location'],
start=dct['start'],
end=dct['end'],
strand=dct['strand'])
gene.save()
stats['n_genes']+=1
prot_accs=[dct['uniprot_accession']]
try:
prot_accs.extend(dct['alt_uniprot_accessions'])
except KeyError:
pass
for acc in prot_accs:
prot=UniprotProtein(id=acc, gene=gene)
prot.save()
stats['n_prots']+=1
print dump(stats)
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'])
