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)
