handlers.py 文件源码

def check_integrity(self):
        from subprocess import check_output
        reads = 0
        try:
            p = check_output("samtools view -c %s" % self.path, shell=True)
            reads = int(p.split("\n")[0].strip())
        except Exception as e:
            print e
            pass

        has_index = False
        has_indate_index = None
        if os.path.exists(self.path + ".bai"):
            has_index = True
            if os.path.getmtime(self.path) <= os.path.getmtime(self.path + ".bai"):
                has_indate_index = True
            else:
                has_indate_index = False

        return {
            ("has_reads", "has 0 reads"): reads > 0,
            ("has_index", "has no BAI"): has_index,
            ("has_indate_index", "has a BAI older than itself"): has_indate_index,
        }