old_contents: import sys
  import trips_client
  from processor import TripsProcessor
  
  
  def process_text(text):
      html = trips_client.send_query(text)
      xml = trips_client.get_xml(html)
      trips_client.save_xml(xml, 'test.xml')
      return process_xml(xml)
  
  
  def process_xml(xml_string):
      tp = TripsProcessor(xml_string)
      tp.get_complexes()
      tp.get_phosphorylation()
      tp.get_activating_mods()
      tp.get_activations()
      return tp
     
  
  if __name__ == '__main__':
      input_fname = 'phosphorylate.xml'
      if len(sys.argv) > 1:
          input_fname = sys.argv[1]
      try:
          fh = open(input_fname, 'rt')
      except IOError:
          print 'Could not open file %s' % input_fname
          sys.exit()
      xml_string = fh.read()
      tp = TripsProcessor(xml_string)
      tp.get_complexes()
      tp.get_phosphorylation()
  
new_contents: import sys
  import trips_client
  from processor import TripsProcessor
  
  
  def process_text(text, save_xml_name='trips_output.xml'):
      html = trips_client.send_query(text)
      xml = trips_client.get_xml(html)
      if save_xml_name:
          trips_client.save_xml(xml, save_xml_name)
      return process_xml(xml)
  
  
  def process_xml(xml_string):
      tp = TripsProcessor(xml_string)
      tp.get_complexes()
      tp.get_phosphorylation()
      tp.get_activating_mods()
      tp.get_activations()
      return tp
     
  
  if __name__ == '__main__':
      input_fname = 'phosphorylate.xml'
      if len(sys.argv) > 1:
          input_fname = sys.argv[1]
      try:
          fh = open(input_fname, 'rt')
      except IOError:
          print 'Could not open file %s' % input_fname
          sys.exit()
      xml_string = fh.read()
      tp = TripsProcessor(xml_string)
      tp.get_complexes()
      tp.get_phosphorylation()
  
subject: Add save xml name argument to TRIPS API