old_contents: # 
  # Author    : Manuel Bernal Llinares
  # Project   : trackhub-creator
  # Timestamp : 28-09-2017 14:20
  # ---
  # © 2017 Manuel Bernal Llinares <mbdebian@gmail.com>
  # All rights reserved.
  # 
  
  """
  This module offers converters between different formats
  """
  
  import abc
  # App imports
  import config_manager
  from parallel.models import ParallelRunner, CommandLineRunnerFactory
  
  
  # Factories
  class DataFormatConverterFactory:
      pass
  
  
  # Possible base class for data format converters
  class DataFormatConverter(ParallelRunner):
      def __init__(self):
          super().__init__()
  
  
  class FileDataFormatConverter(DataFormatConverter):
      def __init__(self):
          super().__init__()
          self.file_path_source = ''
  
  
  class BedToBigBedConverter(FileDataFormatConverter):
      def __init__(self):
          super().__init__()
  
      @abc.abstractmethod
      def _get_command_line_runner(self):
          ...
  
      def _run(self):
          # TODO - Conversion algorithm goes here -
          # TODO - Sort the .bed file
          # TODO - Fetch chromosome sizes for this .bed file
          # TODO - Use bedToBigBed utility to create the .bb (bigBed) file
          pass
  
  
  # Leaves - actual implementations
  class BedToBigBedMultithreadedConverter(BedToBigBedConverter):
      def __init__(self):
          super().__init__()
          self._logger = config_manager.get_app_config_manager() \
              .get_logger_for("{}.{}".format(__name__, type(self).__name__))
  
      def _get_command_line_runner(self):
          return CommandLineRunnerFactory.get_multithread_command_line_runner()
  
  
  class BedToBigBedHpcConverter(BedToBigBedConverter):
      pass
  
  
  if __name__ == '__main__':
      print("ERROR: This script is part of a pipeline collection and it is not meant to be run in stand alone mode")
  
new_contents: # 
  # Author    : Manuel Bernal Llinares
  # Project   : trackhub-creator
  # Timestamp : 28-09-2017 14:20
  # ---
  # © 2017 Manuel Bernal Llinares <mbdebian@gmail.com>
  # All rights reserved.
  # 
  
  """
  This module offers converters between different formats
  """
  
  import abc
  # App imports
  import config_manager
  from parallel.models import ParallelRunner, CommandLineRunnerFactory
  
  
  # Factories
  class DataFormatConverterFactory:
      pass
  
  
  # Possible base class for data format converters
  class DataFormatConverter(ParallelRunner):
      def __init__(self):
          super().__init__()
  
  
  class FileDataFormatConverter(DataFormatConverter):
      def __init__(self):
          super().__init__()
          self.path_source = ''
          self.path_destination = ''
  
  
  class BedToBigBedConverter(FileDataFormatConverter):
      def __init__(self):
          super().__init__()
  
      @abc.abstractmethod
      def _get_command_line_runner(self):
          ...
  
      def _run(self):
          # TODO - Conversion algorithm goes here -
          # TODO - Sort the .bed file
          # TODO - Fetch chromosome sizes for this .bed file
          # TODO - Use bedToBigBed utility to create the .bb (bigBed) file
          pass
  
  
  # Leaves - actual implementations
  class BedToBigBedMultithreadedConverter(BedToBigBedConverter):
      def __init__(self):
          super().__init__()
          self._logger = config_manager.get_app_config_manager() \
              .get_logger_for("{}.{}".format(__name__, type(self).__name__))
  
      def _get_command_line_runner(self):
          return CommandLineRunnerFactory.get_multithread_command_line_runner()
  
  
  class BedToBigBedHpcConverter(BedToBigBedConverter):
      pass
  
  
  if __name__ == '__main__':
      print("ERROR: This script is part of a pipeline collection and it is not meant to be run in stand alone mode")
  
subject: refactor and destination path