old_contents: #!/usr/bin/env python
  
  from sys import stdout, stderr, exit
  from optparse import OptionParser
  from Bio import SeqIO
  
  if __name__ == '__main__':
  
      usage = 'usage: %prog [options] <FASTA FILE>'
      parser = OptionParser(usage=usage)
      parser.add_option('-i', '--ignore_inactive', dest='ignoreInactive',
              help='Ignore fasta records that have been inactivated ' + \
                      'through the [inactivate] tag', action='store_true',
                      default=False) 
      parser.add_option('-c', '--cumulative', dest='cumulative',
              help='Print sum length of fasta records', action='store_true',
              default=False) 
  
      (options, args) = parser.parse_args()
  
      if len(args) != 1:
          parser.print_help()
          exit(1)
  
      c = 0
      for rec in SeqIO.parse(args[0], 'fasta'):
          if not options.ignoreInactive or \
                  not rec.description.endswith('[inactivate]'):
              if options.cumulative:
                  c += len(rec)
              else:
                  print '%s\t%s' %(rec.id, len(rec))
      if options.cumulative:
          print c
  
new_contents: #!/usr/bin/env python
  
  from sys import stdout, stderr, exit
  from optparse import OptionParser
  from Bio import SeqIO
  
  if __name__ == '__main__':
  
      usage = 'usage: %prog [options] <FASTA FILE>'
      parser = OptionParser(usage=usage)
      parser.add_option('-c', '--cumulative', dest='cumulative',
              help='Print sum length of fasta records', action='store_true',
              default=False) 
  
      (options, args) = parser.parse_args()
  
      if len(args) != 1:
          parser.print_help()
          exit(1)
  
      c = 0
      for rec in SeqIO.parse(args[0], 'fasta'):
          if options.cumulative:
              c += len(rec)
          else:
              print '%s\t%s' %(rec.id, len(rec))
      if options.cumulative:
          print c
  
subject: remove obsolete option for "inactive" sequences