" ".join(traceback.print_exc())))
script_util.check_disk_space(self.logger)
# Zip tophat folder
out_file_path = os.path.join(directory, "%s.zip" % output_name)
try:
logger.info("Zipping the output files".format(out_file_path))
script_util.zip_files(self.logger, output_dir, out_file_path)
except Exception, e:
logger.exception(e)
raise Exception(
"Failed to compress the index: {0}".format(out_file_path))
## Upload the file using handle service
try:
#hisat2_handle = hs.upload(out_file_path)
hisat2_handle = script_util.upload_file_to_shock(
logger, out_file_path)['handle']
except Exception, e:
logger.exception(e)
raise Exception("Failed to upload zipped output file".format(
out_file_path))
script_util.check_disk_space(self.logger)
#### Replace version with get_version command#####
logger.info("Preparing output object")
hisat2_out = {
"file": hisat2_handle,
"size": os.path.getsize(out_file_path),
"aligned_using": "hisat2",
"aligner_version": "2.2.6",
'library_type': lib_type,
'condition': condition,
'read_sample_id': read_sample,
except Exception,e:
raise Exception(e)
logger.exception("".join(traceback.format_exc()))
raise Exception("Error parsing FPKMtracking")
## compress and upload to shock
try:
logger.info("Zipping Stringtie output")
print "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:
raise Exception(e)
logger.exception("".join(traceback.format_exc()))
raise Exception("Error executing stringtie")
try:
handle = script_util.upload_file_to_shock(logger,out_file_path)['handle']
except Exception, e:
raise 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:
logger.info("Saving Stringtie object to workspace")
es_obj = { 'id' : output_name,
'type' : 'RNA-Seq',
'numerical_interpretation' : 'FPKM',
'expression_levels' : exp_dict,
'tpm_expression_levels' : tpm_exp_dict,
'processing_comments' : "log2 Normalized",
'genome_id' : genome_id,
'annotation_id' : annotation_id,
prev_value = ''
self.logger.info(line)
except Exception, e:
raise Exception(e)
raise Exception("Error executing cuffdiff {0},{1}".format(
cuffdiff_command, e))
try:
self.logger.info("Zipping Cuffdiff output")
out_file_path = os.path.join(
self.directory,
"{0}.zip".format(self.method_params['output_obj_name']))
script_util.zip_files(self.logger, output_dir, out_file_path)
except Exception, e:
raise Exception("Error executing cuffdiff")
try:
handle = script_util.upload_file_to_shock(self.logger,
out_file_path)['handle']
except Exception, e:
print " ".join(traceback.print_exc())
raise Exception(
"Failed to upload the Cuffdiff output files: {0}".format(
" ".join(traceback.print_exc())))
## Save object to workspace
try:
self.logger.info("Saving Cuffdiff object to workspace")
cm_obj = {
"tool_used": self.tool_used,
"tool_version": self.tool_version,
"condition": self.details['labels'],
"genome_id": self.details['genome_id'],
"expressionSet_id": self.details['expressionset_id'],
"alignmentSet_id": self.details['alignmentset_id'],