old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import argparse
  from target_interaction_finder import TargetInteractionFinder
  
  
  def main():
  
      parser = argparse.ArgumentParser(description='Extract subgraph(s) from XGMML network(s).')
      parser.add_argument('ids',
                          type=str,
                          help='identifier or file path to identifier list')
      parser.add_argument('-c', '--column',
                          default=1,
                          type=int,
                          help='column number for node identifiers in node_ids file (default = 1)')
      parser.add_argument('-s', '--source',
                          default='./source_xgmml/',
                          help='source file or directory path(s) to database XGMML(default = directory named "source_xgmml" in current working directory)')
      parser.add_argument('-t', '--type',
                          default='rna',
                          help='node type (rna or protein; default = rna)')
      parser.add_argument('-o', '--output',
                          default='.',
                          help='output directory path (default = current working directory)')
      parser.add_argument('-d', '--debug',
                          default=False,
                          type=bool, help='Show debug messages')
      args = parser.parse_args()
  
      node_ids = args.ids
      source_xgmml = args.source
      node_id_list_column_index = args.column - 1
      source_type = args.type
      output_dir = args.output
      debug = args.debug
  
      return TargetInteractionFinder(source_xgmml=source_xgmml, node_ids=node_ids, node_id_list_column_index=node_id_list_column_index, output_dir=output_dir, debug=debug)
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import argparse
  from target_interaction_finder import TargetInteractionFinder
  
  
  def main():
  
      parser = argparse.ArgumentParser(description='Extract subgraph(s) from XGMML network(s).')
      parser.add_argument('ids',
                          type=str,
                          help='identifier or file path to identifier list')
      parser.add_argument('-c', '--column',
                          default=1,
                          type=int,
                          help='column number for node identifiers in node_ids file (default = 1)')
      parser.add_argument('-s', '--source',
                          default='./source_xgmml/',
                          help='source file or directory path(s) to database XGMML (default = directory named "source_xgmml" in current working directory)')
      parser.add_argument('-t', '--type',
                          default='rna',
                          help='node type (rna or protein; default = rna)')
      parser.add_argument('-o', '--output',
                          default='.',
                          help='output directory path (default = current working directory)')
      parser.add_argument('-d', '--debug',
                          default=False,
                          type=bool, help='Show debug messages (default = False)')
      args = parser.parse_args()
  
      node_ids = args.ids
      source_xgmml = args.source
      node_id_list_column_index = args.column - 1
      source_type = args.type
      output_dir = args.output
      debug = args.debug
  
      return TargetInteractionFinder(source_xgmml=source_xgmml, node_ids=node_ids, node_id_list_column_index=node_id_list_column_index, output_dir=output_dir, debug=debug)
  
  if __name__ == '__main__':
      main()
  
subject: Clean up.