hisat2-build-new

#!/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()