bowtie2-inspect

#!/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))
    subprocess.call(argv)
        
if __name__ == '__main__':
    main()