Exemple #1
0
    """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,
    )
Exemple #2
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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
Exemple #3
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         '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')
Exemple #4
0
    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()