def _validate(self, params): samt = SamTools(self.config, self.__LOGGER) if 'ignore' in params: path, file = os.path.split(params['file_path']) rval = samt.validate(ifile=file, ipath=path, ignore=params['ignore']) else: path, file = os.path.split(params['file_path']) rval = samt.validate(ifile=file, ipath=path) return rval
def test_invalid_validate(self): samt = SamTools(self.__class__.cfg, self.__class__.__LOGGER) rval = samt.validate(ifile='accepted_hits_invalid.sam', ipath='/kb/module/test/data/samtools') self.assertEquals(1, rval)
def test_valid_validate(self): samt = SamTools(self.__class__.cfg, self.__class__.__LOGGER) rval = samt.validate(ifile='accepted_hits.sam', ipath='/kb/module/test/data/samtools', ignore=['MISSING_READ_GROUP']) self.assertEquals(0, rval)