old_contents: import os
  import shutil
  import glob
  import sys
  from optparse import OptionParser
  import argparse
  
  
  
  
  
  class Options(argparse.ArgumentParser):
      def  __init__(self, prog="sequana_taxonomy"):
          usage = """Welcome to SEQUANA - Taxonomy standalone
  
              sequana_taxonomy --file1 R1.fastq --file2 R2.fastq --database db
  
  AUTHORS: Thomas Cokelaer
  Documentation: http://sequana.readthedocs.io
  Issues: http://github.com/sequana/sequana
          """
          description = """DESCRIPTION:
          """
  
          super(Options, self).__init__(usage=usage, prog=prog,
                  description=description)
  
          # options to fill the config file
          self.add_argument("--file1", dest="file1", type=str,
              help="""R1 fastq file (zipped) """)
          self.add_argument("--file2", dest="file2", type=str,
              help="""R2 fastq file (zipped) """)
          self.add_argument("--database", dest="database", type=str,
              help="""Kraken DB """)
          self.add_argument("--output", dest="output", type=str,
              help="""Kraken DB """, default="krona.html")
          self.add_argument("--thread", dest="thread", type=int,
              help="""number of threads to use """, default=4)
          self.add_argument("--show-html", dest="html", 
              action="store_true", 
              help="""number of threads to use """, default=4)
  
  
  def main(args=None):
  
      if args is None:
          args = sys.argv[:]
  
      user_options = Options(prog="sequana")
  
      # If --help or no options provided, show the help
      if len(args) == 1:
          user_options.parse_args(["prog", "--help"])
      else:
         options = user_options.parse_args(args[1:])
  
      # We put the import here to make the --help faster
      from sequana import KrakenTaxon
  
      fastq = []
      if options.file1:
          fastq.append(options.file1)
      if options.file2:
          fastq.append(options.file2)
      k = KrakenTaxon(fastq, options.database, threads=options.thread, 
              output=options.output)
      k.run()
  
      if options.html is True:
          k.show()
  
  if __name__ == "__main__":
     import sys
     main(sys.argv)
  
  
new_contents: import os
  import shutil
  import glob
  import sys
  from optparse import OptionParser
  import argparse
  
  
  
  
  
  class Options(argparse.ArgumentParser):
      def  __init__(self, prog="sequana_taxonomy"):
          usage = """Welcome to SEQUANA - Taxonomy standalone
  
              sequana_taxonomy --file1 R1.fastq --file2 R2.fastq --database db
  
  AUTHORS: Thomas Cokelaer
  Documentation: http://sequana.readthedocs.io
  Issues: http://github.com/sequana/sequana
          """
          description = """DESCRIPTION:
          """
  
          super(Options, self).__init__(usage=usage, prog=prog,
                  description=description)
  
          # options to fill the config file
          self.add_argument("--file1", dest="file1", type=str,
              help="""R1 fastq file (zipped) """)
          self.add_argument("--file2", dest="file2", type=str,
              help="""R2 fastq file (zipped) """)
          self.add_argument("--database", dest="database", type=str,
              help="""Kraken DB """)
          self.add_argument("--output", dest="output", type=str,
              help="""Kraken DB """, default="krona.html")
          self.add_argument("--thread", dest="thread", type=int,
              help="""number of threads to use """, default=4)
          self.add_argument("--show-html", dest="html", 
              action="store_true", 
              help="""number of threads to use """, default=4)
  
  
  def main(args=None):
  
      if args is None:
          args = sys.argv[:]
  
      user_options = Options(prog="sequana")
  
      # If --help or no options provided, show the help
      if len(args) == 1:
          user_options.parse_args(["prog", "--help"])
      else:
         options = user_options.parse_args(args[1:])
  
      # We put the import here to make the --help faster
      from sequana import KrakenPipeline
  
      fastq = []
      if options.file1:
          fastq.append(options.file1)
      if options.file2:
          fastq.append(options.file2)
      k = KrakenPipeline(fastq, options.database, threads=options.thread, 
              output=options.output)
      k.run()
  
      if options.html is True:
          k.show()
  
  if __name__ == "__main__":
     import sys
     main(sys.argv)
  
  
subject: Use new module