buildConsensus.py 文件源码

def pbdagcon(m5, t):
    script_dir = os.path.dirname(os.path.realpath(__file__))
    cmd = ("%s/pbdagcon -t %d -c 1 -m 1  %s" % (script_dir, t, m5)).split()
    ## hard coded threshold to prevent trimming too many bases
    if(t > 100):
        return None
    proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    ## if in 5 sec, pbdagcon does not finish, trim 1 base and recursively run it
    poll_seconds = 0.25
    deadline = time.time() + 5
    while time.time() < deadline and proc.poll() == None:
        time.sleep(poll_seconds)

    if proc.poll() == None:
        proc.terminate()
        sys.stderr.write("Warning: PBDAGCON timeout! Trimming %d base(s).\n" %(t+1))

    stdout, stderr = proc.communicate()
    if proc.returncode != 0:
        stdout = pbdagcon(m5, t+1)
    return stdout