Python GraphUtils.addMember方法代码示例

# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addMember [as 别名]

#.........这里部分代码省略.........
                    patient_label = ' '.join((affected, gender, relprob))
                    if relprob == 'proband':
                        patient_label = \
                            ' '.join(
                                (patient_label.strip(), 'with', short_desc))
                    else:
                        patient_label = \
                            ' '.join(
                                (patient_label.strip(), 'of proband with',
                                 short_desc))

                    # #############    BUILD THE CELL LINE    #############

                    # Adding the cell line as a typed individual.
                    cell_line_reagent_id = 'CLO:0000031'

                    gu.addIndividualToGraph(
                        g, cell_line_id, line_label, cell_line_reagent_id)

                    # add the equivalent id == dna_ref
                    if dna_ref != '' and dna_ref != catalog_id:
                        equiv_cell_line = 'Coriell:'+dna_ref
                        # some of the equivalent ids are not defined
                        # in the source data; so add them
                        gu.addIndividualToGraph(
                            g, equiv_cell_line, None, cell_line_reagent_id)
                        gu.addSameIndividual(g, cell_line_id, equiv_cell_line)

                    # Cell line derives from patient
                    geno.addDerivesFrom(cell_line_id, patient_id)
                    geno.addDerivesFrom(cell_line_id, cell_type)

                    # Cell line a member of repository
                    gu.addMember(g, repository, cell_line_id)

                    if cat_remark != '':
                        gu.addDescription(g, cell_line_id, cat_remark)

                    # Cell age_at_sampling
                    # TODO add the age nodes when modeled properly in #78
                    # if (age != ''):
                        # this would give a BNode that is an instance of Age.
                        # but i don't know how to connect
                        # the age node to the cell line? we need to ask @mbrush
                        # age_id = '_'+re.sub('\s+','_',age)
                        # gu.addIndividualToGraph(
                        #   g,age_id,age,self.terms['age'])
                        # gu.addTriple(
                        #   g,age_id,self.properties['has_measurement'],age,
                        #   True)

                    # #############    BUILD THE PATIENT    #############

                    # Add the patient ID as an individual.
                    gu.addPerson(g, patient_id, patient_label)
                    # TODO map relationship to proband as a class
                    # (what ontology?)

                    # Add race of patient
                    # FIXME: Adjust for subcategories based on ethnicity field
                    # EDIT: There are 743 different entries for ethnicity...
                    # Too many to map?
                    # Add ethnicity as literal in addition to the mapped race?
                    # Adjust the ethnicity txt (if using)
                    # to initial capitalization to remove ALLCAPS

# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addMember [as 别名]

#.........这里部分代码省略.........
        This will create the instance of a gene that is targeted by a molecular reagent (such as a morpholino or rnai).
        If an instance id is not supplied, we will create it as an anonymous individual which is of the
        type GENO:reagent_targeted_gene.  We will also add the targets relationship between the reagent and gene class.

        <targeted_gene_id> a GENO:reagent_targeted_gene
            rdf:label targeted_gene_label
            dc:description description
        <reagent_id> GENO:targets_instance_of <gene_id>

        :param reagent_id:
        :param gene_id:
        :param targeted_gene_id:
        :return:
        """

        # akin to a variant locus
        if (targeted_gene_id is None):
            targeted_gene_id = '_' + gene_id + '-' + reagent_id
        self.gu.addIndividualToGraph(self.graph, targeted_gene_id, targeted_gene_label,
                                     self.genoparts['reagent_targeted_gene'], description)

        self.gu.addTriple(self.graph, targeted_gene_id,
                          self.object_properties['is_targeted_expression_variant_of'], gene_id)

        self.gu.addTriple(self.graph, targeted_gene_id, self.object_properties['targeted_by'], reagent_id)

        return

    def addTargetedGeneSubregion(self, tgs_id, tgs_label, tgs_type=None, tgs_description=None):
        if tgs_type is None:
            tgs_type = self.genoparts['targeted_gene_subregion']
        self.gu.addIndividualToGraph(self.graph, tgs_id, tgs_label, tgs_type, tgs_description)

    def addMemberOfPopulation(self, member_id, population_id):
        self.gu.addTriple(self.graph, population_id,
                          self.properties['has_member_with_allelotype'], member_id)

        return


    def addTargetedGeneComplement(self, tgc_id, tgc_label, tgc_type=None, tgc_description=None):
        if tgc_type is None:
            tgc_type = self.genoparts['targeted_gene_complement']
        self.gu.addIndividualToGraph(self.graph, tgc_id, tgc_label, tgc_type, tgc_description)

        return


    def addGenome(self, taxon_id, taxon_label=None):
        if taxon_label is None:
            taxon_label = taxon_id
        genome_label = taxon_label+' genome'
        genome_id = self.makeGenomeID(taxon_id)
        self.gu.addClassToGraph(self.graph, genome_id, genome_label, Feature.types['genome'])

        return

    def addReferenceGenome(self, build_id, build_label, taxon_id):
        genome_id = self.makeGenomeID(taxon_id)
        self.gu.addIndividualToGraph(self.graph, build_id, build_label, Feature.types['reference_genome'])
        self.gu.addType(self.graph, build_id, genome_id)
        self.addTaxon(taxon_id, build_id)

        return

    def makeGenomeID(self, taxon_id):