"""This script removes quality and read info from a given SAM file """

import sys
import re
import genome_utils

def parse_options(argv):

    """Parses options from the command line """

    from optparse import OptionParser, OptionGroup

    parser = OptionParser()
    required = OptionGroup(parser, 'REQUIRED')
    required.add_option('-i', '--infile', dest='infile', metavar='FILE', help='input file in SAM format', default='-')
    required.add_option('-o', '--outfile', dest='outfile', metavar='FILE', help='output file in SAM format', default='-')
    optional = OptionGroup(parser, 'OPTIONAL')
    optional.add_option('-q', '--quality_only', dest='quality_only', action='store_true', help='removes only quality information from the SAM file', default=False)
    optional.add_option('-s', '--seq_only', dest='sequence_only', action='store_true', help='removes only sequence information from the SAM file', default=False)
    optional.add_option('-v', '--verbose', dest='verbose', action='store_true', help='verbosity', default=False)
    parser.add_option_group(required)
    parser.add_option_group(optional)

    (options, args) = parser.parse_args()
    
    if len(argv) < 3:
        parser.print_help()
        sys.exit(2)

    return options


def main():
    options = parse_options(sys.argv)

    line_counter = 0
    outf = open(options.outfile, 'w')

    for line in open(options.infile, 'r'):
        line_counter += 1 
        if options.verbose and (line_counter % 10000) == 0:
            print '[ line %s ]' % line_counter

        if line[0] in ['#',  '@']:
            print >> outf, line
            continue

        sl = line.strip().split('\t')

        ### 9 - SEQUENCE
        if not options.quality_only:
            if len(sl) > 9:
                sl[9] = '*'

        ### 10 - QUALITY
        if not options.sequence_only:
            if len(sl) > 10:
                sl[10] = '*'

        ### build up line again
        _line = ''
        for b in sl:
            _line += (b+ '\t')
        print >> outf, _line[:-1]

    outf.close()

if __name__ == '__main__':
    main()