hisat2-inspect

#!/usr/bin/env python

"""
 Copyright 2015, 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 sys
import os
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'
                        )
    inspect_bin_name      = "hisat2-inspect"
    inspect_bin_s         = "hisat2-inspect-s"
    inspect_bin_l         = "hisat2-inspect-l"
    idx_ext_l             = '.1.ht2l'; 
    idx_ext_s             = '.1.ht2'; 
    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)
    options,arguments     = 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 not large_idx_exists and not small_idx_exists:
            env_path = os.getenv('HISAT2_INDEXES', '')
            large_idx_exists = os.path.exists(env_path + '/' + idx_basename + idx_ext_l)
            small_idx_exists = os.path.exists(env_path + '/' + idx_basename + idx_ext_s)

        if large_idx_exists and not small_idx_exists:
            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()