"--gzip-level",
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
parser.add_argument(\
'--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
