new_contents: """
  Convert all the taxonomy IDs to rank so that we are always talking
  about the same thing
  """
  
  import sys
  import taxon
  
  try:
      rank = sys.argv[1]
  except:
      sys.exit(sys.argv[0] + " rank to use ... eg. species or genus")
  
  taxa = taxon.readNodes()
  
  
  
  with open("all_host_taxid.txt", 'r') as rin:
      for l in rin:
          p=l.strip().split("\t")
          ori = p[1]
          while taxa[p[1]].rank != rank and p[1] != '1':
              p[1] = taxa[p[1]].parent
          if p[1] == 1:
              sys.exit("Did not find " + rank + " for " + ori)
          print(p[0] + "\t" + p[1])
  
subject: Convert all the taxonomy IDs to rank so that we are always talking about the same thing