text: #!/usr/bin/env python
  import optparse
  import os
  import sys
  import tempfile
  import shutil
  import subprocess
  import re
  from os.path import basename
  import logging
  
  assert sys.version_info[:2] >= ( 2, 6 )
  
  log = logging.getLogger(__name__)
  working_directory = os.getcwd()
  tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name
  tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name
  
  def stop_err( msg ):
      sys.stderr.write( "%s\n" % msg )
      sys.exit()
  
  def read_stderr():
      stderr = ''
      if(os.path.exists(tmp_stderr_name)):
          with open(tmp_stderr_name, 'rb') as tmp_stderr:
              buffsize = 1048576
              try:
                  while True:
                      stderr += tmp_stderr.read(buffsize)
                      if not stderr or len(stderr) % buffsize != 0:
                          break
              except OverflowError:
                  pass
      return stderr
  
  def execute(command, stdin=None):
      with open(tmp_stderr_name, 'wb') as tmp_stderr:
          with open(tmp_stdout_name, 'wb') as tmp_stdout:
              proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
              returncode = proc.wait()
              if returncode != 0:
                  raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
  
  def delete_file(path):
      if os.path.exists(path):
          try:
              os.remove(path)
          except:
              pass
  
  def delete_directory(directory):
      if os.path.exists(directory):
          try:
              shutil.rmtree(directory)
          except:
              pass
  
  def symlink(source, link_name):
      import platform
      if platform.system() == 'Windows':
          import win32file
          win32file.CreateSymbolicLink(source, link_name, 1)
      else:
          os.symlink(source, link_name)
  
  
  def copy_to_working_directory(data_file, relative_path):
      if os.path.abspath(data_file) != os.path.abspath(relative_path):
          shutil.copy(data_file, relative_path)
      return relative_path
  
  def __main__():
      run_script()
  
  #ENDTEMPLATE
  
  to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2']
  
  def str_to_bool(v):
      """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
      return v.lower() in ["yes", "true", "t", "1"]
  
  
  def run_script():
      parser = optparse.OptionParser()
      parser.add_option('--input', dest='input')
      parser.add_option('--output', dest='output')
      parser.add_option('--fromextension', dest='fromextension')
      parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
      parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
      parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
      parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
      parser.add_option('--noindex', dest='noindex')
      parser.add_option('--zlib', dest='zlib')
      parser.add_option('--filter', dest='filter', action='append', default=[])
  
      (options, args) = parser.parse_args()
  
      filter_commands = ''
      for filter in options.filter:
          filter_commands = "%s --filter \"%s\"" % (filter_commands, filter)
  
      input_file = 'input.%s' % options.fromextension
      copy_to_working_directory(options.input, input_file)
      os.mkdir('output')
      cmd = "msconvert --%s -o output" % (options.toextension)
      if str_to_bool(options.noindex):
          cmd = "%s %s" % (cmd, "--noindex")
      if str_to_bool(options.zlib):
          cmd = "%s %s" % (cmd, "--zlib")
      cmd = "%s --%s" % (cmd, options.binaryencoding)
      cmd = "%s --mz%s" % (cmd, options.mzencoding)
      cmd = "%s --inten%s" % (cmd, options.intensityencoding)
      cmd = "%s %s" % (cmd, input_file)
      cmd = "%s %s" % (cmd, filter_commands)
      print(cmd)
      execute(cmd)
      output_files = os.listdir('output')
      assert len(output_files) == 1
      output_file = output_files[0]
      shutil.copy(os.path.join('output', output_file), options.output)
  
  if __name__ == '__main__': __main__()
  