old_contents: import sys
  import pickle
  from indra import trips
  from indra import reach
  from indra.assemblers import GraphAssembler
  
  
  def process_reach(txt, reread):
      if reread:
          rp = reach.process_text(txt, offline=True)
          st = rp.statements
      else:
          rp = reach.process_json_file('reach_output.json')
          st = rp.statements
      for s in st:
          print('%s\t%s' % (s, s.evidence[0].text))
      return st
  
  def process_trips(txt, reread):
      if reread:
          tp = trips.process_text(txt)
          st = tp.statements
      else:
          tp = trips.process_xml(open('trips_output.xml', 'r').read())
          st = tp.statements
      for s in st:
          print('%s\t%s' % (s, s.evidence[0].text))
      return st
  
  def draw_graph(stmts):
      graphpr = {'rankdir': 'TD'}
      nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
      ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
      ga.make_model()
      ga.save_dot('ras_pathway.dot')
      ga.save_pdf('ras_pathway.pdf')
  
  if __name__ == '__main__':
      reread = True
      txt = open('ras_pathway.txt', 'rt').read()
      print('-----')
      print(txt)
      print('-----')
      if len(sys.argv) < 2:
          print('Reader not specified')
          sys.exit()
      reader = sys.argv[1]
      if reader == 'reach':
          print('Using REACH')
          stmts = process_reach(txt, reread)
      elif reader == 'trips':
          print('Using TRIPS')
          stmts = process_trips(txt, reread)
  
  
new_contents: import sys
  import pickle
  from indra import trips
  from indra import reach
  from indra.assemblers import GraphAssembler
  
  
  def process_reach(txt, reread):
      if reread:
          rp = reach.process_text(txt, offline=True)
          st = rp.statements
      else:
          rp = reach.process_json_file('reach_output.json')
          st = rp.statements
      for s in st:
          print('%s\t%s' % (s, s.evidence[0].text))
      return st
  
  def process_trips(txt, reread):
      if reread:
          tp = trips.process_text(txt)
          st = tp.statements
      else:
          tp = trips.process_xml(open('trips_output.xml', 'r').read())
          st = tp.statements
      for s in st:
          print('%s\t%s' % (s, s.evidence[0].text))
      return st
  
  def draw_graph(stmts):
      graphpr = {'rankdir': 'TD'}
      nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
      ga = GraphAssembler(stmts, graph_properties=graphpr,
                          node_properties=nodepr)
      ga.make_model()
      ga.save_dot('ras_pathway.dot')
      ga.save_pdf('ras_pathway.pdf')
  
  if __name__ == '__main__':
      reread = True
      txt = open('ras_pathway.txt', 'rt').read()
      print('-----')
      print(txt)
      print('-----')
      if len(sys.argv) < 2:
          print('Reader not specified')
          sys.exit()
      reader = sys.argv[1]
      if reader == 'reach':
          print('Using REACH')
          stmts = process_reach(txt, reread)
      elif reader == 'trips':
          print('Using TRIPS')
          stmts = process_trips(txt, reread)
  
  
subject: Fix GraphAssembler input argument