'--stranded', action='store_const', const=True, default=False,
help='Assume input reads come from the sense strand; then partitions '
'in output have terminal + and - indicating sense strand')
parser.add_argument('--score-min', type=int, required=False,
default=48,
help='Bowtie2 minimum CONSTANT score to use')
parser.add_argument('--gzip-level', type=int, required=False,
default=3,
help='Gzip compression level to use for temporary Bowtie input file')
parser.add_argument('--intermediate-dir', type=str, required=False,
default='./',
help='Where to put transcript index if it needs to be downloaded')
# Add command-line arguments for dependencies
bowtie.add_args(parser)
filemover.add_args(parser)
tempdel.add_args(parser)
# Collect Bowtie arguments, supplied in command line after the -- token
argv = sys.argv
bowtie2_args = ''
in_args = False
for i, argument in enumerate(sys.argv[1:]):
if in_args:
bowtie2_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
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
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])