docs: def show_seq(clus_obj, index):
      """Get the precursor and map sequences to it.
         this way we create a positional map."""
      current = clus_obj.clus
      clus_seqt = clus_obj.seq
      clus_locit = clus_obj.loci
  
      itern = 0
      for idc in current.keys():
          itern += 1
          timestamp = str(idc)
          seqListTemp = ()
          f = open("/tmp/"+timestamp+".fa","w")
          for idl in current[idc].loci2seq.keys():
              seqListTemp = list(set(seqListTemp).union(current[idc].loci2seq[idl]))
          maxscore = 0
          for s in seqListTemp:
              score = calculate_size(clus_seqt[s].freq)
              maxscore = max(maxscore,score)
              clus_seqt[s].score = score
              seq = clus_seqt[s]
              f.write(">"+s+"\n"+seq.seq+"\n")
          f.close()
  
          locilen_sorted = sorted(current[idc].locilen.iteritems(), key = operator.itemgetter(1),reverse = True)
          lmax = clus_locit[locilen_sorted[0][0]]
          f = open("/tmp/"+timestamp+".bed","w")
          f.write("%s\t%s\t%s\t.\t.\t%s\n" % (lmax.chr,lmax.start,lmax.end,lmax.strand))
          f.close()
          os.system("bedtools  getfasta -s -fi "+index+" -bed /tmp/"+timestamp+".bed -fo /tmp/"+timestamp+".pre.fa")
          os.system("bowtie2-build /tmp/"+timestamp+".pre.fa  /tmp/"+timestamp+".pre.ind >/dev/null 2>&1")
          os.system("bowtie2 --rdg 7,3 --mp 4 --end-to-end --no-head --no-sq  -D 20 -R 3 -N 0 -i S,1,0.8 -L 3 -f /tmp/"+timestamp+".pre.ind /tmp/"+timestamp+".fa -S /tmp/"+timestamp+".map  >>bowtie.log 2>&1")
          f = open("/tmp/"+timestamp+".map","r")
          seqpos = {}
          minv = 10000000
          for line in f:
              line = line.strip()
              cols = line.split("\t")
              seqpos[cols[0]] = int(cols[3])
              if minv>int(cols[3]):
                  minv = int(cols[3])
          f.close()
          seqpos_sorted = sorted(seqpos.iteritems(), key = operator.itemgetter(1),reverse = False)
          showseq = ""
          showseq_plain = ""
          for (s,pos) in seqpos_sorted:
              ratio = (clus_seqt[s].score*1.0/maxscore*100.0)
              realScore = (math.log(ratio,2)*2)
              if realScore<0:
                  realScore = 0
              # "score %s max %s  ratio %s real %.0f" % (clus_seqt[s].score,maxscore,ratio,realScore)
              ##calculate the mean expression of the sequence and change size letter
              showseq_plain += "<br>%s<a style = \"font-size:%.0fpx;\"href = javascript:loadSeq(\"%s\")>%s</a>" % ("".join("." for i in range(pos-1)),realScore+10,s,clus_seqt[s].seq)
              #showseq+ = seqviz.addseq(pos-1,clus_seqt[s].len,clus_seqt[s].seq)
          #current[idc].showseq = showseq
          current[idc].showseq_plain = showseq_plain
          os.system("rm /tmp/"+timestamp+"*")
      clus_obj.clus = current
      clus_obj.seq = clus_seqt
      return clus_obj