old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import cPickle as pickle
  import bz2
  import json
  import argparse
  
  def transform_json_to_pkl(args):
      with open(args.json_input, 'r') as json_file:
          json_str = json_file.read()
          metadata = json.loads(json_str)
  
          for marker in metadata["markers"]:
              metadata["markers"][marker]["ext"] = set(metadata["markers"][marker]["ext"])
  
      pkl_output = bz2.BZ2File(args.pkl_output, 'w')
      pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
      pkl_output.close()
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser()
      parser.add_argument('--json_input', required=True)
      parser.add_argument('--pkl_output', required=True)
      
      args = parser.parse_args()
  
      transform_json_to_pkl(args)
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import cPickle as pickle
  import bz2
  import json
  import argparse
  
  
  def transform_json_to_pkl(args):
      with open(args.json_input, 'r') as json_file:
          json_str = json_file.read()
          metadata = json.loads(json_str)
  
          for marker in metadata["markers"]:
              a_set = set(metadata["markers"][marker]["ext"])
              metadata["markers"][marker]["ext"] = a_set
  
      pkl_output = bz2.BZ2File(args.pkl_output, 'w')
      pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
      pkl_output.close()
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser()
      parser.add_argument('--json_input', required=True)
      parser.add_argument('--pkl_output', required=True)
      args = parser.parse_args()
  
      transform_json_to_pkl(args)
  
subject: Fix flake8 for tools/metaphlan2/transform_json_to_pkl.py