massivePhrap.py 文件源码

def run(self):
        try: 
            proc_name = self.name
            #Open the bams
            nBams = [] # nonTrim Bams
            tBams = [] # trim Bams
            for i in self.args.bam:
                nBams.append(pysam.Samfile(i))
            for i in self.args.pacBam:
                tBams.append(pysam.Samfile(i))

            while True:
                next_task = self.task_queue.get()
                if next_task is None:
                    # Poison pill means shutdown
                    logging.info('Thread %s: Exiting\n' % proc_name)
                    self.task_queue.task_done()
                    break
                try:
                    answer = next_task(nBams, tBams)
                except Exception as e:
                    logging.error("Exception raised in task %s" % (str(e)))
                    self.task_queue.task_done()
                    self.result_queue.put("Failure - UNK - %s" % str(e))
                    logging.info("fail in groupid=%s" % next_task.data.name)
                    continue
                self.task_queue.task_done()
                self.result_queue.put(answer)
            return
        except Exception as e:
            logging.error("Consumer %s Died\nERROR: %s" % (self.name, e))
            return