bakH.py 文件源码

def test(argv):
    numpy.seterr(all="ignore")
    args = parseArgs(argv)
    setupLogging(True)#keep debug on.. you're testing!
    logging.critical(("Running HSpots.py directly implements testing mode. "
                      "If you're trying to run the full, actual program, use "
                      "Honey.py spots"))

    bam = pysam.Samfile(args.bam)
    reference = pysam.Fastafile(args.reference)
    try:
        if bam.header["HD"]["SO"] != "coordinate":
            logging.warning("BAM is not sorted by coordinates! Performance may be slower")
    except KeyError:
        logging.warning("Assuming BAM is sorted by coordinate. Be sure this is correct")
    logging.info("Running in test mode")

    #do what you will.. from here
    #spot = SpotResult(chrom='11', start=2215290, end=2215798, svtype="DEL", size=208)
    #spot = SpotResult(chrom='22', start=45964261, end=45965596, svtype="DEL", size=-1)
    # This is what I need to start with
    #spot = SpotResult(chrom="22", start=45963975, end=45964532, svtype="DEL", size=57)
    fh = open("honeymissing.bed")
    for line in fh.readlines():
        data = line.strip().split('\t')
        spot = SpotResult(chrom=data[0], start=int(data[1]), end = int(data[2]), \
                          size=int(data[3].split('=')[-1]), svtype="DEL")

        j = SpotCaller('group', spot.chrom, spot.start, spot.end, args)
        if j.supportingReadsFilter(spot, bam, args):
            consen = ConsensusCaller(spot, args)
            consen(bam, reference, 'none')
            for i in consen.newSpots:
                i.tags["seqmade"] = True
                print i
            if len(consen.newSpots) == 0:
                spot.tags["noseq"] = True
                print str(spot)
        else:
            spot.tags["filtfail"] = True
            print str(spot)

    #done with test code
    logging.info("Finished testing")