1.1 --- a/utils/markup_to_file.py	Thu Jun 14 20:24:26 2012 +0400
     1.2 +++ b/utils/markup_to_file.py	Fri Jun 29 19:34:21 2012 +0400
     1.3 @@ -50,6 +50,18 @@
     1.4      if options.markups:
     1.5          options.markups = options.markups.split(",")
     1.6  
     1.7 -    main()
     1.8 +    if args and (options.input_file != "-" or options.output_file != "-"):
     1.9 +        parser.error("Either specify positional arguments, or -i/-o, never both")
    1.10 +
    1.11 +    if args:
    1.12 +        for arg in args:
    1.13 +            options.input_file = arg
    1.14 +            if arg.endswith(".markup"):
    1.15 +                arg = arg[:-len(".markup")]
    1.16 +            options.output_file = arg + ".fasta"
    1.17 +            sys.stderr.write("{0} -> {1}\n".format(options.input_file, options.output_file))
    1.18 +            main()
    1.19 +    else:
    1.20 +        main()
    1.21  
    1.22  # vim: set et ts=4 sts=4 sw=4: