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."""
args = parser.parse_args(argv[1:])
# Start keep_alive thread immediately
if args.keep_alive:
from dooplicity.tools import KeepAlive
keep_alive_thread = KeepAlive(sys.stderr)
keep_alive_thread.start()
if __name__ == "__main__":
import time
start_time = time.time()
go(
bowtie_exe=os.path.expandvars(args.bowtie_exe),
bowtie_index_base=os.path.expandvars(args.bowtie_idx),
bowtie_args=bowtie_args,
gzip_level=args.gzip_level,
verbose=args.verbose,
report_multiplier=args.report_multiplier,
scratch=tempdel.silentexpandvars(args.scratch),
)
'--type', type=int, required=False, default=1,
help='If 1, assume final fields are ints. If 2, assume final fields '
'are floats. Otherwise, assume final fields are strings.'
)
parser.add_argument(
'--keep-alive', action='store_const', const=True,
default=False,
help='Periodically print Hadoop status messages to stderr to keep ' \
'job alive'
)
args = parser.parse_args()
if args.keep_alive:
from dooplicity.tools import KeepAlive
keep_alive_thread = KeepAlive(sys.stderr)
input_line_count, output_line_count = 0, 0
# Must consume a line of stdin before outputting status messages
line = sys.stdin.readline()
if args.keep_alive: keep_alive_thread.start()
if args.type == 1:
last_key, totals, write_line = None, [0] * args.value_count, False
while True:
if not line:
if last_key is None:
# Input is empty
break
else:
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
different command-line arguments can be passed to it for unit tests.'''
args = parser.parse_args(argv[1:])
mover = filemover.FileMover(args=args)
# Start keep_alive thread immediately
if args.keep_alive:
from dooplicity.tools import KeepAlive
keep_alive_thread = KeepAlive(sys.stderr)
keep_alive_thread.start()
if __name__ == '__main__' and not args.test:
import time
start_time = time.time()
go(bowtie2_exe=os.path.expandvars(args.bowtie2_exe),
bowtie2_index_base=os.path.expandvars(args.bowtie2_idx),
bowtie2_args=bowtie2_args,
verbose=args.verbose,
report_multiplier=args.report_multiplier,
stranded=args.stranded,
fudge=args.fudge,
score_min=args.score_min,
mover=mover,
intermediate_dir=args.intermediate_dir,
'--type', type=int, required=False, default=1,
help='If 1, assume final fields are ints. If 2, assume final fields '
'are floats. Otherwise, assume final fields are strings.'
)
parser.add_argument(
'--keep-alive', action='store_const', const=True,
default=False,
help='Periodically print Hadoop status messages to stderr to keep ' \
'job alive'
)
args = parser.parse_args()
if args.keep_alive:
from dooplicity.tools import KeepAlive
keep_alive_thread = KeepAlive(sys.stderr)
input_line_count, output_line_count = 0, 0
# Must consume a line of stdin before outputting status messages
line = sys.stdin.readline()
if args.keep_alive: keep_alive_thread.start()
if args.type == 1:
last_key, totals, write_line = None, [0]*args.value_count, False
while True:
if not line:
if last_key is None:
# Input is empty
break
else: