code: def run(self):
          '''
          Change to a temp directory
          Run bash script containing commands
          Place results in specified output file
          Clean up temp directory
          '''
          qry = os.path.abspath(self.qry)
          ref = os.path.abspath(self.ref)
          outfile = os.path.abspath(self.outfile)
          tmpdir = tempfile.mkdtemp(prefix='tmp.run_nucmer.', dir=os.getcwd())
          original_dir = os.getcwd()
          os.chdir(tmpdir)
          script = 'run_nucmer.sh'
          self._write_script(script, ref, qry, outfile)
          syscall.run('bash ' + script, verbose=self.verbose)
          os.chdir(original_dir)
          shutil.rmtree(tmpdirf run(self):
          '''
          Change to a temp directory
          Run bash script containing commands
          Place results in specified output file
          Clean up temp directory
          '''
          qry = os.path.abspath(self.qry)
          ref = os.path.abspath(self.ref)
          outfile = os.path.abspath(self.outfile)
          tmpdir = tempfile.mkdtemp(prefix='tmp.run_nucmer.', dir=os.getcwd())
          original_dir = os.getcwd()
          os.chdir(tmpdir)
          script = 'run_nucmer.sh'
          self._write_script(script, ref, qry, outfile)
          syscall.run('bash ' + script, verbose=self.verbose)
          os.chdir(original_dir)
          shutil.rmtree(tmpdir)
docs: Change to a temp directory
          Run bash script containing commands
          Place results in specified output file
          Clean up temp directory