101 lines
3.0 KiB
Plaintext
101 lines
3.0 KiB
Plaintext
|
#!/usr/bin/env python
|
||
|
|
|
||
|
|
"""
|
||
|
|
Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
|
||
|
|
|
||
|
|
This file is part of HISAT 2.
|
||
|
|
|
||
|
|
HISAT 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.
|
||
|
|
|
||
|
|
HISAT 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 HISAT 2. 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 == '--large-index':
|
||
|
|
parsed_args[arg] = ""
|
||
|
|
to_remove.append(i)
|
||
|
|
elif 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
|
||
|
|
constuct_bin_name = "hisat2-construct-nonrepetitive-genome"
|
||
|
|
constuct_bin_s = "hisat2-construct-nonrepetitive-genome-s"
|
||
|
|
constuct_bin_l = "hisat2-construct-nonrepetitive-genome-l"
|
||
|
|
build_bin_name = "hisat2-build"
|
||
|
|
build_bin_s = "hisat2-build-s"
|
||
|
|
build_bin_l = "hisat2-build-l"
|
||
|
|
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'
|
||
|
|
|
||
|
|
if '--large-index' in options:
|
||
|
|
build_bin_spec = os.path.join(ex_path,build_bin_l)
|
||
|
|
elif len(argv) >= 2:
|
||
|
|
ref_fnames = argv[-2]
|
||
|
|
tot_size = 0
|
||
|
|
for fn in ref_fnames.split(','):
|
||
|
|
if os.path.exists(fn):
|
||
|
|
statinfo = os.stat(fn)
|
||
|
|
tot_size += statinfo.st_size
|
||
|
|
if tot_size > small_index_max_size:
|
||
|
|
build_bin_spec = os.path.join(ex_path,build_bin_l)
|
||
|
|
|
||
|
|
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()
|
||
|
|
|
||
|
|
|