code: def pasa(args):
      
      p = OptionParser(pasa.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      pasa_db, fastafile = args
  
      termexons = "pasa.terminal_exons.gff3"
      if need_update(fastafile, termexons):
          cmd = "$ANNOT_DEVEL/PASA2/scripts/pasa_asmbls_to_training_set.dbi"
          cmd += ' -M "{0}:mysql.tigr.org" -p "access:access"'.format(pasa_db)
          cmd += ' -g {0}'.format(fastafile)
          sh(cmd)
  
          cmd = "$EVM/PasaUtils/retrieve_terminal_CDS_exons.pl"
          cmd += " trainingSetCandidates.fasta trainingSetCandidates.gff"
          sh(cmd, outfile=termexons)
  
      return termexons
docs: %prog pasa pasa_db fastafile
  
      Run EVM in TIGR-only mode.