code: def neighbor(args):
      
      p = OptionParser(neighbor.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      agpfile, componentID = args
      fastadir = "fasta"
  
      cmd = "grep"
      cmd += " --color -C2 {0} {1}".format(componentID, agpfile)
      sh(cmd)
  
      agp = AGP(agpfile)
      aorder = agp.order
      if not componentID in aorder:
          print("Record {0} not present in `{1}`."\
                  .format(componentID, agpfile), file=sys.stderr)
          return
  
      i, c = aorder[componentID]
      north, south = agp.getNorthSouthClone(i)
  
      if not north.isCloneGap:
          ar = [north.component_id, componentID, "--dir=" + fastadir]
          if north.orientation == '-':
              ar += ["--qreverse"]
          overlap(ar)
  
      if not south.isCloneGap:
          ar = [componentID, south.component_id, "--dir=" + fastadir]
          if c.orientation == '-':
              ar += ["--qreverse"]
          overlap(ar)
docs: %prog neighbor agpfile componentID
  
      Check overlaps of a particular component in agpfile.