"""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),
)
print >>sys.stderr, "DONE with align_readlets.py; in=%d; " "time=%0.3f s" % (
_input_line_count,
time.time() - start_time,
)
import time
start_time = time.time()
input_line_count = 0
if args.out is not None:
'''If --out is a local file, just write directly to that file. Otherwise,
write to a temporary file that will later be uploaded to the
destination.'''
output_url = Url(args.out)
if output_url.is_local:
try: os.makedirs(output_url.to_url())
except: pass
output_filename = os.path.join(args.out, args.junction_filename)
else:
temp_dir_path = make_temp_dir(tempdel.silentexpandvars(args.scratch))
register_cleanup(tempdel.remove_temporary_directories,
[temp_dir_path])
output_filename = args.junction_filename + '.temp'
output_filename = os.path.join(temp_dir_path, output_filename)
with xopen(True, output_filename, 'w', args.gzip_level) as output_stream:
for line in sys.stdin:
tokens = line.strip().split('\t')
# Remove leading zeros from ints
print >>output_stream, '\t'.join(
[tokens[0], str(int(tokens[1])),
str(int(tokens[2]) - 1), tokens[3], tokens[4]]
)
input_line_count += 1
else:
# Default --out is stdout
'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:
os.makedirs(os.path.join(temp_dir_path, 'index'))
except:
pass
# Write to temporary directory, and later upload to URL
index_basename = os.path.join(temp_dir_path, 'index/' + args.basename)
fasta_file = os.path.join(temp_dir_path, 'temp.fa')
print >> sys.stderr, 'Opened %s for writing....' % fasta_file
with open(fasta_file, 'w') as fasta_stream:
input_line_count = 0
for line in sys.stdin:
counter.add('inputs')
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,
scratch=tempdel.silentexpandvars(args.scratch))
print >>sys.stderr, ('DONE with cointron_enum.py; in=%d; time=%0.3f s') % \
(_input_line_count, time.time() - start_time)
elif __name__ == '__main__':
# Test units
del sys.argv[1:] # Don't choke on extra command-line parameters
import unittest
# Add unit tests here
unittest.main()
