def Main(): global args,out CellLine=["H1"] HM=("input","H3K27ac","H3K27me3","H3K36me3","H3K4me1","H3K4me3","H3K9me3") marks=[] dbi={} args=ParseArg() if args.output=="stdout": out=sys.stdout else: try: out=open(args.output,"w") except IOError: print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead" out=sys.stdout for cell in CellLine: for hm in HM: mark=cell+"_"+hm marks.append(mark) dbi[mark]=DBI.init("/data/zhuxp/bam2x/data/bamlist/"+mark+".bamlist","bamlist") for i,x in enumerate(TableIO.parse(args.input,args.input_format)): print >>out,"QR\t",x if i%100==0: print >>sys.stderr,"query %d entries\r"%i, for mark in marks: print >>out,mark,"\t" for j in DBI.query(x,dbi[mark]): print >>out,"HT\t",j
def Main(): global args,out args=ParseArg() if args.output=="stdout": out=sys.stdout else: try: out=open(args.output,"w") except IOError: print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead" out=sys.stdout dbi=DBI.init(args.db,args.dbformat) for x in TableIO.parse(args.input,args.input_format): print "QR\t",x for j in DBI.query(x,dbi): print "HT\t",j x.chr=x.chr.replace("chr","") for j in DBI.query(x,dbi): print "HT\t",j