def parse(self, limit=None):
        """
        Override Source.parse()
        Args:
            :param limit (int, optional) limit the number of rows processed
        Returns:
            :return None
        """
        if limit is not None:
            LOG.info("Only parsing first %d rows", limit)

        phenotype_file = '/'.join(
            (self.rawdir, self.files['patient_phenotypes']['file']))
        variant_file = '/'.join((self.rawdir, self.files['patient_variants']['file']))

        phenotype_file_handler = open(phenotype_file, 'r')
        variant_file_handler = open(variant_file, 'r')

        self._parse_patient_phenotypes(phenotype_file_handler, limit)
        self._parse_patient_variants(variant_file_handler)

        return
def parse ( self , limit = None ) : if limit is not None : LOG . info ( "Only parsing first %d rows" , limit ) phenotype_file = '/' . join ( ( self . rawdir , self . files [ 'patient_phenotypes' ] [ 'file' ] ) ) variant_file = '/' . join ( ( self . rawdir , self . files [ 'patient_variants' ] [ 'file' ] ) ) phenotype_file_handler = open ( phenotype_file , 'r' ) variant_file_handler = open ( variant_file , 'r' ) self . _parse_patient_phenotypes ( phenotype_file_handler , limit ) self . _parse_patient_variants ( variant_file_handler ) return
Override Source.parse()
        Args:
            :param limit (int, optional) limit the number of rows processed
        Returns:
            :return None