hisatgenotype_toolkit

#!/usr/bin/env python
# --------------------------------------------------------------------------- #
# Copyright 2017, Daehwan Kim <infphilo@gmail.com>                            #
#                                                                             #
# This file is part of HISAT-genotype. Its purpose is as a wrapper for        #
# secondary and individual scripts in HISATgenotype                           #
#                                                                             #
# HISAT-genotype 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-genotype 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-genotype.  If not, see <http://www.gnu.org/licenses/>.     #
# --------------------------------------------------------------------------- #

import sys
import os
import subprocess
import re 
import resource
import inspect
import random
import math
from datetime import datetime, date, time
from argparse import ArgumentParser, FileType
import hisatgenotype_typing_common as typing_common

# --------------------------------------------------------------------------- #
# Main function for wrapper that contains all functions                       #
# --------------------------------------------------------------------------- #
if __name__ == '__main__':
    # This step is critical for finding the scripts to run
    path = '/'.join(os.path.realpath(__file__).split('/')[:-1])
    path += '/hisatgenotype_tools/'
    if not os.path.exists(path):
        print('Error! Toolkit Directory not found at %s' % path,
              file=sys.stderr)
        exit(1)

    scripts = []
    sfiles = sorted(os.listdir(path))
    for script in sfiles:
        if script.startswith('.'):
            continue
        scripts.append(script)
    
    parser = ArgumentParser(
        description='HISAT-genotype Toolkit')
    parser.add_argument('--see-script',
                      dest='see_script',
                      action='store_true',
                      help='Prints the exact script and options being run')
    subparser = parser.add_subparsers(title='Tools',
                                      dest='script',
                                      help='HISAT-genotype tools and \
                                                individual scripts')

    subparsers = []
    script_key = {}
    for itr in range(len(scripts)):
        # Need to strip the file name and get the core of the script name
        name = scripts[itr]\
            .replace('hisatgenotype_', '')\
            .replace('run_', '')\
            .replace('_', '-')\
                .split('.')[0]
        script = scripts[itr]

        script_key.update({ name : script })

        subparsers.append(subparser.add_parser(name, 
                                               help=script,
                                               add_help=False))

        subparsers[itr].add_argument('-h', '--help',
                                     dest='script_help', 
                                     action='store_true' 
                                     )
        
    args, additional = parser.parse_known_args()
    
    cmd = [path]
    cmd[0] += script_key[args.script]
    if additional and not args.script_help:
        cmd += additional
    elif args.script_help:
        cmd += additional + ['--help']
    elif args.script not in ['conc-results']:
        print("Please provide options for tool selected", 
              file=sys.stderr)
        exit(1)    

    if args.see_script:
        print(cmd)
    code = subprocess.call(cmd)
    if code != 0:
        print('Script exited with error %d' % code)