methods.py 文件源码

def find_roi_bam(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