def vep(self):
        """VEP"""

        # calculate time thread took to finish
        # logging.info('Starting VEP ')
        tstart = datetime.now()

        vep_obj = vep.Vep(self.vcf_file)
        std = vep_obj.run()

        # command = 'python %s/vep.py -i sanity_check/checked.vcf' % (scripts_dir)
        # self.shell(command)

        # command = 'mv vep/vep.log log/'
        # os.system(command)

        # command = 'mv vep/vep.output.vcf_summary.html reports/vep_summary.html'
        # os.system(command)

        tend = datetime.now()
        execution_time = tend - tstart
def vep ( self ) : tstart = datetime . now ( ) vep_obj = vep . Vep ( self . vcf_file ) std = vep_obj . run ( ) tend = datetime . now ( ) execution_time = tend - tstart
VEP