def _process_gene_marker_relationships(self, limit=None):
        """
        Gene-marker relationships include:
            clone contains gene,
            coding sequence of,
            contains polymorphism,
            gene contains small segment,
            gene encodes small segment,
            gene has artifact,
            gene hybridized by small segment,
            gene produces transcript,
            gene product recognized by antibody,
            knockdown reagent targets gene,
            promoter of,
            transcript targets gene

        Here, we only process the following:
            knockdown reagent targets gene,
            coding sequence of,
            promoter of,
            transcript targets gene

        We only take a fraction of these here...
        we are interested in the knockdown reagents, promoters, and
        the transgenic constructs with coding bits.

        :param limit:
        :return:

        """

        if self.test_mode:
            graph = self.testgraph
        else:
            graph = self.graph
        model = Model(graph)
        LOG.info("Processing gene marker relationships")
        line_counter = 0
        raw = '/'.join((self.rawdir, self.files['gene_marker_rel']['file']))
        geno = Genotype(graph)

        with open(raw, 'r', encoding="iso-8859-1") as csvfile:
            filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')
            for row in filereader:
                line_counter += 1

                (gene_id, gene_so_id, gene_symbol, marker_id, marker_so_id,
                 marker_symbol, relationship
                 # , empty
                ) = row

                if self.test_mode and not (
                        gene_id in self.test_ids['gene'] or
                        marker_id in self.test_ids['allele'] or
                        marker_id in self.test_ids['morpholino']):
                    continue

                # there are many relationships, but we only take a few for now
                if relationship in [
                        'knockdown reagent targets gene',
                        'coding sequence of',
                        'gene product recognized by antibody',
                        'promoter of',
                        'transcript targets gene']:
                    gene_id = 'ZFIN:' + gene_id.strip()
                    geno.addGene(gene_id, gene_symbol, gene_so_id)

                    marker_id = 'ZFIN:' + marker_id.strip()
                    if relationship == 'knockdown reagent targets gene':
                        geno.addGeneTargetingReagent(
                            marker_id, marker_symbol, marker_so_id, gene_id)
                        # waiting to add the reagent_targeted_gene
                        # until processing environments

                    elif relationship == 'coding sequence of':
                        # we add the partonomy
                        # directly to the allele in the process_fish method
                        geno.addConstruct(
                            marker_id, marker_symbol, marker_so_id)
                        transgene_part_id = self._make_transgene_part_id(
                            marker_id, gene_id, relationship)
                        transgene_part_label = 'Tg('+relationship+' '+gene_symbol+')'
                        model.addIndividualToGraph(
                            transgene_part_id, transgene_part_label,
                            self.globaltt['coding_transgene_feature'])
                        geno.addSequenceDerivesFrom(transgene_part_id, gene_id)

                        # save the transgenic parts in a hashmap for later
                        if marker_id not in self.transgenic_parts:
                            self.transgenic_parts[marker_id] = set()
                        self.transgenic_parts[marker_id].add(transgene_part_id)
                        self.id_label_map[transgene_part_id] = transgene_part_label

                    elif relationship == 'gene product recognized by antibody':
                        # TODO for ticket #32
                        pass
                    elif relationship == 'promoter of':
                        # transgenic constructs with promoters regions
                        # we add the partonomy
                        # directly to the allele in the process_fish method
                        geno.addConstruct(marker_id, marker_symbol, marker_so_id)
                        transgene_part_id = self._make_transgene_part_id(
                            marker_id, gene_id, relationship)
                        transgene_part_label = 'Tg(' + relationship + ' ' +\
                            gene_symbol + ')'
                        model.addIndividualToGraph(
                            transgene_part_id, transgene_part_label,
                            self.globaltt['regulatory_transgene_feature'])
                        geno.addSequenceDerivesFrom(transgene_part_id, gene_id)

                        # save the transgenic parts in a hashmap for later
                        if marker_id not in self.transgenic_parts:
                            self.transgenic_parts[marker_id] = set()
                        self.transgenic_parts[marker_id].add(transgene_part_id)

                    elif relationship == 'transcript targets gene':  # miRNAs
                        # TODO should this be an interaction
                        # instead of this special relationship?
                        model.addIndividualToGraph(
                            marker_id, marker_symbol, marker_so_id)
                        graph.addTriple(
                            marker_id, self.globaltt['targets_gene'], gene_id)
                    else:
                        pass

                self.id_label_map[marker_id] = marker_symbol
                # just in case we haven't seen it before
                self.id_label_map[gene_id] = gene_symbol

                if not self.test_mode and limit is not None and line_counter > limit:
                    break

        LOG.info("Done with gene marker relationships")
        return
Gene-marker relationships include:
            clone contains gene,
            coding sequence of,
            contains polymorphism,
            gene contains small segment,
            gene encodes small segment,
            gene has artifact,
            gene hybridized by small segment,
            gene produces transcript,
            gene product recognized by antibody,
            knockdown reagent targets gene,
            promoter of,
            transcript targets gene

        Here, we only process the following:
            knockdown reagent targets gene,
            coding sequence of,
            promoter of,
            transcript targets gene

        We only take a fraction of these here...
        we are interested in the knockdown reagents, promoters, and
        the transgenic constructs with coding bits.

        :param limit:
        :return: