parameters: (self)
docstring: This function calls all needed steps for running the analysis.
docstring_summary: This function calls all needed steps for running the analysis.
docstring_tokens: This function calls all needed steps for running the analysis .
function: def run_analysis(self):
          """
          This function calls all needed steps for running the analysis.
          """
  
          super(TranscriptomeAnalysis, self).run_analysis()
  
          if self._restart:
              checkpoint = self.get_checkpoint(
                  reset_random_suffix=True)
              TranscriptomeAnalysis._logger.warning(
                  'Restarting an uncompleted run')
          else:
              checkpoint = 0  # all steps will be done
          if checkpoint < 1:
              TranscriptomeAnalysis._logger.info(
                  '****** Step 1/2, current time: %s ******' %
                  time.strftime("%m/%d/%Y %H:%M:%S"))
              if self._has_variants_file:
                  self._run_tblastn(
                      ancestral_variants=True)
              else:
                  self._run_tblastn(
                      ancestral_variants=False)
              self._set_checkpoint(1)
          TranscriptomeAnalysis._logger.info(
              '****** Step 2/2, current time: %s ******' %
              time.strftime("%m/%d/%Y %H:%M:%S"))
          self._load_score()
          self._load_length()
          self._get_coordinates()
          self._run_hmmer()
          self._produce_short_summary()
          self.cleanup()
          if self._tarzip:
              self._run_tarzip_hmmer_output()
              self._run_tarzip_translated_proteins()
          # remove the checkpoint, run is done
          self._set_checkpoint()
function_tokens: def run_analysis ( self ) : super ( TranscriptomeAnalysis , self ) . run_analysis ( ) if self . _restart : checkpoint = self . get_checkpoint ( reset_random_suffix = True ) TranscriptomeAnalysis . _logger . warning ( 'Restarting an uncompleted run' ) else : checkpoint = 0 # all steps will be done if checkpoint < 1 : TranscriptomeAnalysis . _logger . info ( '****** Step 1/2, current time: %s ******' % time . strftime ( "%m/%d/%Y %H:%M:%S" ) ) if self . _has_variants_file : self . _run_tblastn ( ancestral_variants = True ) else : self . _run_tblastn ( ancestral_variants = False ) self . _set_checkpoint ( 1 ) TranscriptomeAnalysis . _logger . info ( '****** Step 2/2, current time: %s ******' % time . strftime ( "%m/%d/%Y %H:%M:%S" ) ) self . _load_score ( ) self . _load_length ( ) self . _get_coordinates ( ) self . _run_hmmer ( ) self . _produce_short_summary ( ) self . cleanup ( ) if self . _tarzip : self . _run_tarzip_hmmer_output ( ) self . _run_tarzip_translated_proteins ( ) # remove the checkpoint, run is done self . _set_checkpoint ( )