new_contents: #!/usr/bin/env python
  
  import os,sys
  import argparse
  import logging.config
  
  from biomaj.utils import Utils
  
  def main():
  
    parser = argparse.ArgumentParser()
  
    parser.add_argument('-s', '--scan', dest="directory",help="Directory to scan")
    parser.add_argument('--type', dest="ftype",help="Files type")
    parser.add_argument('--tags', dest="tags", action="append", default=[],
         help="tags, format key:value, can be repeated multiple times")
  
    args = parser.parse_args()
  
    if not os.path.exists(args.directory):
        sys.exit(1)
  
    res = {}
    for (path, dirs, files) in os.walk(args.directory):
        for file in files:
          filename = os.path.join(path, file)
          (file_format, mime) = Utils.detect_format(filename)
          if file_format is not None:
            file_format = file_format.replace('application/','')
          filename = filename.replace(args.directory+'/','')
          if file_format is not None:
            if file_format not in res:
              res[file_format] = [filename]
            else:
              res[file_format].append(filename)
  
    f_type = ''
    if args.ftype:
      f_type = args.ftype
    tags = ''
    if args.tags:
      tags = ','.join(args.tags)
    for fformat in res.keys():
      print '##BIOMAJ#'+fformat+'#'+f_type+'#'+tags+'#'+','.join(res[fformat])
  
  
  if __name__ == '__main__':
      main()
  
subject: add helper process scan.py to scan files in a directory , autodetect format and add to process output for metadata