def main(argv=None):

    if not argv:
        argv = sys.argv

    # setup command line parser
    parser = E.OptionParser(version="%prog version: $Id$",
                            usage=globals()["__doc__"])

    parser.add_option(
        "-g", "--gtf-file", dest="filename_gtf", type="string",
        help="filename with gene models in gtf format [%default]")

    parser.add_option(
        "-m", "--filename-mismapped", dest="filename_mismapped", type="string",
        help="output bam file for mismapped reads [%default]")

    parser.add_option(
        "-j", "--junctions-bed-file", dest="filename_junctions", type="string",
        help="bam file with reads mapped across junctions [%default]")

    parser.add_option(
        "-r", "--filename-regions", dest="filename_regions", type="string",
        help="filename with regions to remove in bed format [%default]")

    parser.add_option(
        "-t", "--transcripts-gtf-file", dest="filename_transcriptome",
        type="string",
        help="bam file with reads mapped against transcripts [%default]")

    parser.add_option(
        "-p", "--map-tsv-file", dest="filename_map", type="string",
        help="filename mapping transcript numbers (used by "
        "--filename-transciptome) to transcript names "
        "(used by --filename-gtf) [%default]")

    parser.add_option(
        "-s", "--filename-stats", dest="filename_stats", type="string",
        help="filename to output stats to [%default]")

    parser.add_option(
        "-o", "--colour",
        dest="colour_mismatches", action="store_true",
        help="mismatches will use colour differences (CM tag) [%default]")

    parser.add_option(
        "-i", "--ignore-mismatches",
        dest="ignore_mismatches", action="store_true",
        help="ignore mismatches [%default]")

    parser.add_option(
        "-c", "--remove-contigs", dest="remove_contigs", type="string",
        help="','-separated list of contigs to remove [%default]")

    parser.add_option(
        "-f", "--force-output", dest="force", action="store_true",
        help="force overwriting of existing files [%default]")

    parser.add_option("-u", "--unique", dest="unique", action="store_true",
                      help="remove reads not matching uniquely [%default]")

    parser.add_option("--output-sam", dest="output_sam", action="store_true",
                      help="output in sam format [%default]")

    parser.set_defaults(
        filename_gtf=None,
        filename_mismapped=None,
        filename_junctions=None,
        filename_transcriptome=None,
        filename_map=None,
        remove_contigs=None,
        force=False,
        unique=False,
        colour_mismatches=False,
        ignore_mismatches=False,
        output_sam=False,
        filename_table=None,
    )

    # add common options (-h/--help, ...) and parse command line
    (options, args) = E.Start(parser, argv=argv)

    if len(args) != 1:
        raise ValueError("please supply one bam file")

    bamfile_genome = args[0]
    genome_samfile = pysam.Samfile(bamfile_genome, "rb")

    if options.remove_contigs:
        options.remove_contigs = options.remove_contigs.split(",")

    if options.filename_map:
        E.info("reading map")
        id_map = IOTools.readMap(
            IOTools.openFile(options.filename_map), has_header=True)
        id_map = dict([(y, x) for x, y in id_map.iteritems()])
    else:
        id_map = None

    transcripts = {}
    if options.filename_gtf:
        E.info("indexing geneset")
        mapped, missed = 0, 0
        for gtf in GTF.transcript_iterator(
                GTF.iterator(IOTools.openFile(options.filename_gtf))):
            gtf.sort(key=lambda x: x.start)
            transcript_id = gtf[0].transcript_id
            if id_map:
                try:
                    transcript_id = id_map[transcript_id]
                    mapped += 1
                except KeyError:
                    missed += 1
                    continue
            transcripts[transcript_id] = gtf

        E.info("read %i transcripts from geneset (%i mapped, %i missed)" %
               (len(transcripts), mapped, missed))

    regions_to_remove = None
    if options.filename_regions:
        E.info("indexing regions")
        regions_to_remove = IndexedGenome.Simple()
        for bed in Bed.iterator(IOTools.openFile(options.filename_regions)):
            regions_to_remove.add(bed.contig, bed.start, bed.end)
        E.info("read %i regions" % len(regions_to_remove))

    if options.filename_transcriptome:
        transcripts_samfile = pysam.Samfile(options.filename_transcriptome,
                                            "rb")
    else:
        transcripts_samfile = None

    if options.output_sam:
        output_samfile = pysam.Samfile("-", "wh", template=genome_samfile)
    else:
        output_samfile = pysam.Samfile("-", "wb", template=genome_samfile)

    if options.filename_mismapped:
        if not options.force and os.path.exists(options.filename_mismapped):
            raise IOError("output file %s already exists" %
                          options.filename_mismapped)
        output_mismapped = pysam.Samfile(options.filename_mismapped,
                                         "wb",
                                         template=genome_samfile)
    else:
        output_mismapped = None

    if options.filename_junctions:
        junctions_samfile = pysam.Samfile(options.filename_junctions,
                                          "rb")
    else:
        junctions_samfile = None

    c = _bams2bam.filter(genome_samfile,
                         output_samfile,
                         output_mismapped,
                         transcripts_samfile,
                         junctions_samfile,
                         transcripts,
                         regions=regions_to_remove,
                         unique=options.unique,
                         remove_contigs=options.remove_contigs,
                         colour_mismatches=options.colour_mismatches,
                         ignore_mismatches=options.ignore_mismatches,
                         ignore_transcripts=transcripts_samfile is None,
                         ignore_junctions=junctions_samfile is None)

    if options.filename_stats:
        outf = IOTools.openFile(options.filename_stats, "w")
        outf.write("category\tcounts\n%s\n" % c.asTable())
        outf.close()

    if options.filename_transcriptome:
        transcripts_samfile.close()

    genome_samfile.close()
    output_samfile.close()
    if output_mismapped:
        output_mismapped.close()

    # write footer and output benchmark information.
    E.Stop()
Open and return a spy on an object. Will automatically create a stub
dataset/ETHPy150Open CGATOxford/cgat/scripts/bams2bam.py/main--crossover with--dataset/ETHPy150Open agoragames/chai/chai/chai.py/ChaiBase.spy