/usr/bin/bowtie-inspect is in bowtie 1.1.2-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | #!/usr/bin/env python
"""
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 imp
import inspect
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 = imp.load_source('bowtie-build',os.path.join(ex_path,'bowtie-build'))
options,arguments = bld.build_args()
if '--verbose' in options:
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()
|