bowtie-inspect

#!/usr/bin/env python3

"""
 Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>

 This file is part of Bowtie.

 Bowtie 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 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.  If not, see <http://www.gnu.org/licenses/>.
"""


import os
import inspect
from importlib.machinery import SourceFileLoader
import logging

def main():
    logging.basicConfig(level=logging.ERROR,
                        format='%(levelname)s: %(message)s'
                        )
    inspect_bin_name      = "bowtie-inspect"
    inspect_bin_s         = "bowtie-inspect-s"
    inspect_bin_l         = "bowtie-inspect-l"
    idx_ext_l             = '.1.ebwtl'
    idx_ext_s             = '.1.ebwt'
    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)
    bld                   = SourceFileLoader('bowtie-build',os.path.join(ex_path,'bowtie-build')).load_module()
    options,arguments     = bld.build_args()

    if '--verbose' in options:
        arguments.append('--verbose')
        logging.getLogger().setLevel(logging.INFO)

    if '--debug' in options:
        inspect_bin_spec += '-debug'
        inspect_bin_l += '-debug'

    if '--large-index' in options:
        inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
    elif len(arguments) >= 1:
        idx_basename = arguments[-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:
            logging.info("No small index but a large one is present. Inspecting the large index.")
            inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)

    arguments[0] = inspect_bin_name
    arguments.insert(1, 'basic-0')
    arguments.insert(1, '--wrapper')
    logging.info('Command: %s %s' %  (inspect_bin_spec,' '.join(arguments[1:])))
    os.execv(inspect_bin_spec, arguments)


if __name__ == "__main__":
    main()