1#!/usr/local/bin/python3.8
2
3"""
4 Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
5
6 This file is part of Bowtie.
7
8 Bowtie is free software: you can redistribute it and/or modify
9 it under the terms of the GNU General Public License as published by
10 the Free Software Foundation, either version 3 of the License, or
11 (at your option) any later version.
12
13 Bowtie is distributed in the hope that it will be useful,
14 but WITHOUT ANY WARRANTY; without even the implied warranty of
15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16 GNU General Public License for more details.
17
18 You should have received a copy of the GNU General Public License
19 along with Bowtie.  If not, see <http://www.gnu.org/licenses/>.
20"""
21
22
23import os
24import inspect
25from importlib.machinery import SourceFileLoader
26import logging
27
28def main():
29    logging.basicConfig(level=logging.ERROR,
30                        format='%(levelname)s: %(message)s'
31                        )
32    inspect_bin_name      = "bowtie-inspect"
33    inspect_bin_s         = "bowtie-inspect-s"
34    inspect_bin_l         = "bowtie-inspect-l"
35    idx_ext_l             = '.1.ebwtl'
36    idx_ext_s             = '.1.ebwt'
37    curr_script           = os.path.realpath(inspect.getsourcefile(main))
38    ex_path               = os.path.dirname(curr_script)
39    inspect_bin_spec      = os.path.join(ex_path,inspect_bin_s)
40    bld                   = SourceFileLoader('bowtie-build',os.path.join(ex_path,'bowtie-build')).load_module()
41    options,arguments     = bld.build_args()
42
43    if '--verbose' in options:
44        arguments.append('--verbose')
45        logging.getLogger().setLevel(logging.INFO)
46
47    if '--debug' in options:
48        inspect_bin_spec += '-debug'
49        inspect_bin_l += '-debug'
50
51    if '--large-index' in options:
52        inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
53    elif len(arguments) >= 1:
54        idx_basename = arguments[-1]
55        large_idx_exists = os.path.exists(idx_basename + idx_ext_l)
56        small_idx_exists = os.path.exists(idx_basename + idx_ext_s)
57        if large_idx_exists and not small_idx_exists:
58            logging.info("No small index but a large one is present. Inspecting the large index.")
59            inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
60
61    arguments[0] = inspect_bin_name
62    arguments.insert(1, 'basic-0')
63    arguments.insert(1, '--wrapper')
64    logging.info('Command: %s %s' %  (inspect_bin_spec,' '.join(arguments[1:])))
65    os.execv(inspect_bin_spec, arguments)
66
67
68if __name__ == "__main__":
69    main()
70