type=int, required=False, default=3, help=("Level of gzip compression to use for temporary file storing " "qnames."), ) parser.add_argument( "--keep-alive", action="store_const", const=True, default=False, help="Periodically print Hadoop status messages to stderr to keep " "job alive", ) # Add command-line arguments for dependencies bowtie.add_args(parser) tempdel.add_args(parser) # Collect Bowtie arguments, supplied in command line after the -- token argv = sys.argv bowtie_args = "" in_args = False for i, argument in enumerate(sys.argv[1:]): if in_args: bowtie_args += argument + " " if argument == "--": argv = sys.argv[: i + 1] in_args = True """Now collect other arguments. While the variable args declared below is global, properties of args are also arguments of the go() function so different command-line arguments can be passed to it for unit tests."""
'--out', metavar='URL', type=str, required=False, default='None', help='Bowtie index files are written to this URL. DEFAULT IS CURRENT ' 'WORKING DIRECTORY.') parser.add_argument(\ '--basename', type=str, required=False, default='junction', help='Basename for index to be written') parser.add_argument(\ '--keep-alive', action='store_const', const=True, default=False, help='Prints reporter:status:alive messages to stderr to keep EMR ' 'task alive') filemover.add_args(parser) bowtie.add_args(parser) tempdel.add_args(parser) args = parser.parse_args() import time start_time = time.time() output_filename, output_stream, output_url = [None] * 3 output_url = Url(args.out) if args.out is not None \ else Url(os.getcwd()) # Set up temporary destination import tempfile temp_dir_path = make_temp_dir(tempdel.silentexpandvars(args.scratch)) # For deleting temporary directory, even on unexpected exit register_cleanup(tempdel.remove_temporary_directories, [temp_dir_path]) # Set up temporary destination try: