# -*- coding: utf-8 -*-
"""
Glimmer --> extract
version 0.2 (andrea.pinna@crs4.it)
"""

import optparse
import subprocess
import sys

def __main__():
    # load arguments
    print 'Parsing Extract input options...'
    parser = optparse.OptionParser()
    parser.add_option('--exSequence', dest='sequence', help='')
    parser.add_option('--exCoords', dest='coords', help='')
    parser.add_option('--ex2Fields', action='store_true', dest='twofields', help='')
    parser.add_option('--exDir', action='store_true', dest='dir', help='')
    parser.add_option('--exMinLen', dest='minlen', type='int', help='')
    parser.add_option('--exNoStart', action='store_true', dest='nostart', help='')
    parser.add_option('--exNoStop', action='store_true', dest='nostop', help='')
    parser.add_option('--exNoWrap', action='store_true', dest='nowrap', help='')
    parser.add_option('--exOutput', dest='output', help='')
    parser.add_option('--logfile', dest='logfile', help='')
    (options, args) = parser.parse_args()
    if len(args) > 0:
        parser.error('Wrong number of arguments')
    
    # build Extract command to be executed
    sequence = options.sequence
    coords = options.coords
    if options.twofields:
        twofields = '--2_fields'
    else:
        twofields = ''
    if options.dir:
        direct = '--dir'
    else:
        direct = ''
    if options.minlen is not None:
        minlen = '--minlen %d' % (options.minlen)
    else:
        minlen = ''
    if options.nostart:
        nostart = '--nostart'
    else:
        nostart = ''
    if options.nostop:
        nostop = '--nostop'
    else:
        nostop = ''
    if options.nowrap:
        nowrap = '--nowrap'
    else:
        nowrap = ''
    output = options.output
    logfile = options.logfile
    
    # Build Extract command
    cmd = 'extract %s %s %s %s %s %s %s %s > %s' % (twofields, direct, minlen, nostart, nostop, nowrap, sequence, coords, output)
    print '\nExtract command to be executed: \n %s' % (cmd)
    
    print 'Executing Extract...'
    if logfile:
        log = open(logfile, 'w')
    else:
        log = sys.stdout
    try:
        subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
    finally:
        if log != sys.stdout:
            log.close()
    print 'Extract executed!'


if __name__ == "__main__":
    __main__()