old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  """
  The output file is <input-file>.ct
  """
  from __future__ import print_function
  import textwrap
  import argparse
  import subprocess
  
  def exe(cmd):
      o = subprocess.Popen(
          cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
      out = o.stdout.read().strip().decode()
      err = o.stderr.read().strip().decode()
      return out, err
  
  def dot2ct():
      pass
  
  
  def get_parser():
      parser = argparse.ArgumentParser(
          description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
  
      parser.add_argument("-v", "--verbose",
                          action="store_true", help="be verbose")
      parser.add_argument("file", help=textwrap.dedent("""Input is:
  >seq
  aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
  ((...((((((((((.......)))))))))).))
  """))
      return parser
  
  if __name__ == '__main__':
      parser = get_parser()
      args = parser.parse_args()
  
      cmd='dot2ct ' + args.file + ' ' + args.file + '.ct'
      out, err= exe(cmd)
      print(out, end='')
      if not err:
          print(' Created: %s' % args.file + '.ct')
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  """
  The output file is <input-file>.ct
  
  Wrapper to
  
  RNAstructure: software for RNA secondary structure prediction and analysis. (2010). RNAstructure: software for RNA secondary structure prediction and analysis., 11, 129. http://doi.org/10.1186/1471-2105-11-129
  """
  from __future__ import print_function
  import textwrap
  import argparse
  import subprocess
  
  def exe(cmd):
      o = subprocess.Popen(
          cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
      out = o.stdout.read().strip().decode()
      err = o.stderr.read().strip().decode()
      return out, err
  
  def dot2ct():
      pass
  
  
  def get_parser():
      parser = argparse.ArgumentParser(
          description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
  
      parser.add_argument("-v", "--verbose",
                          action="store_true", help="be verbose")
      parser.add_argument("file", help=textwrap.dedent("""Input is:
  >seq
  aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
  ((...((((((((((.......)))))))))).))
  """))
      return parser
  
  if __name__ == '__main__':
      parser = get_parser()
      args = parser.parse_args()
  
      cmd='dot2ct ' + args.file + ' ' + args.file + '.ct'
      out, err= exe(cmd)
      print(out, end='')
      if not err:
          print(' Created: %s' % args.file + '.ct')
  
subject: add ref