Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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
Ejemplo n.º 3
0
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)