def run_DESeq2(input_path, out_path, DESeq_negatives_to_zero):
 if DESeq_negatives_to_zero:
  command_args = [('-i %s -o %s -z %s' % (input_path, out_path, DESeq_negatives_to_zero))]
 else:
  command_args = [('-i %s -o %s' % (input_path, out_path))]
 rsl = RExecutor(TmpDir=get_qiime_temp_dir())
 app_result = rsl(command_args=command_args, script_name='DESeq2.r')
 return app_result

def run_DESeq2 ( input_path , out_path , DESeq_negatives_to_zero ) : if DESeq_negatives_to_zero : command_args = [ ( '-i %s -o %s -z %s' % ( input_path , out_path , DESeq_negatives_to_zero ) ) ] else : command_args = [ ( '-i %s -o %s' % ( input_path , out_path ) ) ] rsl = RExecutor ( TmpDir = get_qiime_temp_dir ( ) ) app_result = rsl ( command_args = command_args , script_name = 'DESeq2.r' ) return app_result
run deseq2 negative binomial wald algorithm through rscript .