old_contents: import copy
  import glob
  import logging
  import os
  import subprocess
  from plugins import BaseAssessment
  from yapsy.IPlugin import IPlugin
  
  class AleAssessment(BaseAssessment, IPlugin):
      def run(self):
          """ 
          Build the command and run.
          Return list of file(s)
          """
          contigs = self.data.contigfiles[0]
          exp = '(bowtie2 (contigs {}) READS)'.format(contigs)
          samfile = self.plugin_engine.run_expression(exp).files[0]
          cmd_args = [self.executable, samfile, contigs,
                      os.path.join(self.outpath, 'ale.txt')]
          self.arast_popen(cmd_args)
          report = os.path.join(self.outpath, 'ale.txt')
          output = {}
          if os.path.exists(report):
              output['report'] =  report
              ## Parse report for ALE Score
              with open(report) as r:
                  output['ale_score'] = r.readline().split(' ')[2].strip()
          return output
  
  
  
new_contents: import copy
  import glob
  import logging
  import os
  import subprocess
  from plugins import BaseAssessment
  from yapsy.IPlugin import IPlugin
  
  class AleAssessment(BaseAssessment, IPlugin):
      def run(self):
          """ 
          Build the command and run.
          Return list of file(s)
          """
          contigs = self.data.contigfiles[0]
          exp = '(bowtie2 (contigs {}) READS)'.format(contigs)
          samfile = self.plugin_engine.run_expression(exp).files[0]
          cmd_args = [self.executable, samfile, contigs,
                      os.path.join(self.outpath, 'ale.txt')]
          self.arast_popen(cmd_args)
          report = os.path.join(self.outpath, 'ale.txt')
          output = {}
          if os.path.exists(report):
              output['report'] =  report
              ## Parse report for ALE Score
              with open(report) as r:
                  output['ale_score'] = float(r.readline().split(' ')[2].strip())
          return output
  
  
  
subject: fix ale score