stderr = ret["stderr"] prev_value = "" for line in stderr.splitlines(False): if line.startswith("> Processing Locus"): words = line.split() cur_value = words[len(words) - 1] if prev_value != cur_value: logger.info(line) # print line else: prev_value = "" logger.info(line) # print line ##Parse output files exp_dict = script_util.parse_FPKMtracking(os.path.join(output_dir, "genes.fpkm_tracking"), "Cufflinks", "FPKM") ## compress and upload to shock try: logger.info("Zipping Cufflinks output") out_file_path = os.path.join(directory, "%s.zip" % output_name) script_util.zip_files(logger, output_dir, out_file_path) except Exception, e: logger.exception("".join(traceback.format_exc())) raise Exception("Error executing cufflinks") try: handle = hs.upload(out_file_path) except Exception, e: logger.exception("".join(traceback.format_exc())) raise Exception("Error while zipping the output objects: {0}".format(out_file_path)) ## Save object to workspace try:
prev_value = '' for line in stderr.splitlines(False): if line.startswith('> Processing Locus'): words = line.split() cur_value = words[len(words) - 1] if prev_value != cur_value: logger.info(line) #print line else: prev_value = '' logger.info(line) #print line ##Parse output files exp_dict = script_util.parse_FPKMtracking( os.path.join(output_dir, "genes.fpkm_tracking"), 'Cufflinks', 'FPKM') ## compress and upload to shock try: logger.info("Zipping Cufflinks output") out_file_path = os.path.join(directory, "%s.zip" % output_name) script_util.zip_files(logger, output_dir, out_file_path) except Exception, e: logger.exception("".join(traceback.format_exc())) raise Exception("Error executing cufflinks") try: handle = hs.upload(out_file_path) except Exception, e: logger.exception("".join(traceback.format_exc())) raise Exception( "Error while zipping the output objects: {0}".format(
if 'gap_sep_value' in params and params['gap_sep_value'] is not None: stringtie_command += (' -g '+str(params['gap_sep_value'])) if 'disable_trimming' in params and params['disable_trimming'] != 0: stringtie_command += (' -t ') if 'ballgown_mode' in params and params['ballgown_mode'] != 0: stringtie_command += (' -B ') if 'skip_reads_with_no_ref' in params and params['skip_reads_with_no_ref'] != 0: stringtie_command += (' -e ') t_file_name = os.path.join(output_dir,"transcripts.gtf") g_output_file = os.path.join(output_dir,"genes.fpkm_tracking") stringtie_command += " -o {0} -A {1} -G {2} {3}".format(t_file_name,g_output_file,gtf_file,input_file) logger.info("Executing: stringtie {0}".format(stringtie_command)) ret = script_util.runProgram(None,"stringtie",stringtie_command,None,directory) ##Parse output files try: exp_dict = script_util.parse_FPKMtracking(g_output_file,'StringTie','FPKM') tpm_exp_dict = script_util.parse_FPKMtracking(g_output_file,'StringTie','TPM') except Exception,e: logger.exception("".join(traceback.format_exc())) raise Exception("Error parsing FPKMtracking") ## compress and upload to shock try: logger.info("Zipping Stringtie output") out_file_path = os.path.join(directory,"%s.zip" % output_name) script_util.zip_files(logger,output_dir,out_file_path) except Exception,e: logger.exception("".join(traceback.format_exc())) raise Exception("Error executing stringtie") try: handle = hs.upload(out_file_path)