def main(): args = docopt(__doc__) #print(args) bam_f = args['--bam'] include_f = args['--include'] exclude_f = args['--exclude'] out_prefix = args['--out'] read_format = args['--read_format'] if not read_format in set(['fq', 'fa']): sys.exit("[X] Read format must be fq or fa!") noninterleaved = args['--noninterleaved'] include_unmapped = True if args['--exclude_unmapped']: include_unmapped = False out_f = BtIO.getOutFile(bam_f, out_prefix, None) if include_f and exclude_f: print(BtLog.error('43')) elif include_f: sequence_list = BtIO.parseList(include_f) BtIO.parseBamForFilter(bam_f, include_unmapped, noninterleaved, out_f, sequence_list, None, read_format) elif exclude_f: sequence_list = BtIO.parseList(exclude_f) BtIO.parseBamForFilter(bam_f, include_unmapped, noninterleaved, out_f, None, sequence_list, read_format) else: BtIO.parseBamForFilter(bam_f, include_unmapped, noninterleaved, out_f, None, None, read_format)
def main(): args = docopt(__doc__) bam_f = args['--bam'] include_f = args['--include'] exclude_f = args['--exclude'] out_prefix = args['--out'] include_unmapped = args['--include_unmapped'] gzip = None do_sort = args['--sort'] keep_sorted = args['--keep'] sort_threads = int(args['--threads']) out_f = BtIO.getOutFile(bam_f, out_prefix, None) if include_f and exclude_f: print BtLog.error('43') elif include_f: sequence_list = BtIO.parseList(include_f) BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, sequence_list, None, gzip, do_sort, keep_sorted, sort_threads) elif exclude_f: sequence_list = BtIO.parseList(exclude_f) BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, None, sequence_list, gzip, do_sort, keep_sorted, sort_threads) else: BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, None, None, gzip, do_sort, keep_sorted, sort_threads)