code: def fastq_touchup_for_vsearch_merge(read, outfile, reverse=False):
      
      
      counts = 0
      with open(outfile, 'w') as out:
          ## read in paired end read files 4 lines at a time
          if read.endswith(".gz"):
              fr1 = gzip.open(read, 'rb')
          else:
              fr1 = open(read, 'rb')
          quarts = itertools.izip(*[iter(fr1)]*4)
  
          ## a list to store until writing
          writing = []
  
          while 1:
              try:
                  lines = quarts.next()
              except StopIteration:
                  break
              if reverse:
                  seq = lines[1].strip()[::-1]
              else:
                  seq = lines[1].strip()
              writing.append("".join([
                  lines[0],
                  seq+"\n",
                  lines[2],
                  "B"*len(seq)
              ]))
  
              ## write to disk
              counts += 1
              if not counts % 1000:
                  out.write("\n".join(writing)+"\n")
                  writing = []
          if writing:
              out.write("\n".join(writing))
              
      out.close()
      fr1.close()
docs: option to change orientation of reads and sets Qscore to B