methods.py 文件源码

def find_roi_amp(chromosome_event):
    chr, event = chromosome_event.split("_")
    roi, sortbyname, sortbyCoord, hetsnp = init_file_names(chr, event, tmpbams_path, haplotype_path)
    exonsinroibed = "/".join([haplotype_path, event + "_exons_in_roi_" + chr + '.bed'])
    success = True
    try:
        if not terminating.is_set():
            roisort = sub('.bam$', '.sorted', roi)
            if (os.path.isfile(exonsinroibed)):
                cmd = " ".join(["sort -u", exonsinroibed, "-o", exonsinroibed]);
                runCommand(cmd)
                extractPairedReadfromROI(sortbyname, exonsinroibed, roi)
                removeIfEmpty(tmpbams_path, ntpath.basename(roi))
                pysam.sort(roi, roisort)
                pysam.index(roisort + '.bam')
                os.remove(roi)

    except (KeyboardInterrupt):
        logger.error('Exception Crtl+C pressed in the child process  in find_roi_bam for chr ' + chr + event)
        terminating.set()
        success = False
        return
    except Exception as e:
        logger.exception("Exception in find_roi_bam %s", e)
        terminating.set()
        success = False
        return
    if (success):
        logger.debug("find_roi_bam complete successfully for " + chr + event)
    return