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#!/usr/bin/env python
"""
Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
This file is part of Bowtie 2.
Bowtie 2 is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Bowtie 2 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
"""
import os
import imp
import inspect
import logging
import argparse
import subprocess
from collections import deque
def main():
parser = argparse.ArgumentParser()
group = parser.add_mutually_exclusive_group()
group.add_argument('--debug', action='store_true')
group.add_argument('--sanitized', action='store_true')
parser.add_argument('--verbose', action='store_true')
parser.add_argument('--large-index', action='store_true')
logging.basicConfig(level=logging.ERROR,
format='%(levelname)s: %(message)s'
)
inspect_bin_name = 'bowtie-inspect'
inspect_bin_s = 'bowtie2-inspect-s'
inspect_bin_l = 'bowtie2-inspect-l'
idx_ext_l = '.1.bt2l';
idx_ext_s = '.1.bt2';
curr_script = os.path.realpath(inspect.getsourcefile(main))
ex_path = os.path.dirname(curr_script)
inspect_bin_spec = os.path.join(ex_path,inspect_bin_s)
script_options, argv = parser.parse_known_args()
argv = deque(argv)
if script_options.verbose:
logging.getLogger().setLevel(logging.INFO)
if script_options.debug:
inspect_bin_spec += '-debug'
inspect_bin_l += '-debug'
if script_options.sanitized:
inpsect_bin_spec += '-sanitized'
inspect_bin_l += '-sanitized'
if script_options.large_index:
inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
elif len(argv) >= 1:
idx_basename = argv[-1]
large_idx_exists = os.path.exists(idx_basename + idx_ext_l)
small_idx_exists = os.path.exists(idx_basename + idx_ext_s)
if large_idx_exists and not small_idx_exists:
inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
argv.appendleft('basic-0')
argv.appendleft('--wrapper')
argv.appendleft(inspect_bin_spec)
logging.info('Command: %s' % ' '.join(argv))
print argv
subprocess.call(argv)
if __name__ == '__main__':
main()
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