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#!/usr/bin/env python
"""
Copyright 2014, Daehwan Kim <infphilo@gmail.com>
This file is part of Centrifuge, which is copied and modified from bowtie2 in the Bowtie2 package.
Centrifuge 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.
Centrifuge 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 Centrifuge. If not, see <http://www.gnu.org/licenses/>.
"""
import os
import sys
import inspect
import logging
def build_args():
"""
Parse the wrapper arguments. Returns the options,<programm arguments> tuple.
"""
parsed_args = {}
to_remove = []
argv = sys.argv[:]
for i, arg in enumerate(argv):
if arg == '--debug':
parsed_args[arg] = ""
to_remove.append(i)
elif arg == '--verbose':
parsed_args[arg] = ""
to_remove.append(i)
for i in reversed(to_remove):
del argv[i]
return parsed_args, argv
def main():
logging.basicConfig(level=logging.ERROR,
format='%(levelname)s: %(message)s'
)
delta = 200
small_index_max_size= 4 * 1024**3 - delta
build_bin_name = "centrifuge-build-bin"
build_bin_s = "centrifuge-build-bin"
curr_script = os.path.realpath(inspect.getsourcefile(main))
ex_path = os.path.dirname(curr_script)
build_bin_spec = os.path.join(ex_path,build_bin_s)
options, argv = build_args()
if '--verbose' in options:
logging.getLogger().setLevel(logging.INFO)
if '--debug' in options:
build_bin_spec += '-debug'
build_bin_l += '-debug'
argv[0] = build_bin_name
argv.insert(1, 'basic-0')
argv.insert(1, '--wrapper')
logging.info('Command: %s %s' % (build_bin_spec, ' '.join(argv[1:])))
os.execv(build_bin_spec, argv)
if __name__ == "__main__":
main()
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