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 main(args):
print args
genelist=readgenes(args.tripnegs_fn)
print '%d trip-neg genes' % len(genelist)
g2s=gene2synonyms(args.gene2syn_fn)
def get_targets(gene_sym):
genes=[gene_sym]
try: genes.extend(g2s.g2s[gene_sym])
except KeyError: pass
targets=[]
syms=[]
for gene in genes:
ts=Target.objects.filter(gene_sym=gene)
if len(ts)>0:
targets.extend(ts)
syms.append(gene)
return targets,syms
for gene in genelist:
targets=get_targets(gene)[0]
if len(targets)>0:
print 'gene %s: %d targets' % (gene, len(targets))
for target in targets:
drugs=target.drugs.all()
print ' target: %s (%d drugs)' % (target, len(drugs))
for drug in drugs:
print ' drug: %s' % drug
print
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)
