Python Model.addDeprecatedClass方法代码示例

# 需要导入模块: from dipper.models.Model import Model [as 别名]
# 或者: from dipper.models.Model.Model import addDeprecatedClass [as 别名]
    def process_gene_ids(self, limit):
        raw = '/'.join((self.rawdir, self.files['gene_ids']['file']))

        if self.testMode:
            g = self.testgraph
        else:
            g = self.graph

        model = Model(g)
        logger.info("Processing: %s", self.files['gene_ids']['file'])
        line_counter = 0
        geno = Genotype(g)
        with gzip.open(raw, 'rb') as csvfile:
            filereader = csv.reader(
                io.TextIOWrapper(csvfile, newline=""), delimiter=',',
                quotechar='\"')
            for row in filereader:
                line_counter += 1
                (taxon_num,
                 gene_num,
                 gene_symbol,
                 gene_synonym,
                 live,
                 gene_type) = row
                # 6239,WBGene00000001,aap-1,Y110A7A.10,Live,protein_coding_gene

                if self.testMode and gene_num not in self.test_ids['gene']:
                    continue

                taxon_id = 'NCBITaxon:'+taxon_num
                gene_id = 'WormBase:'+gene_num
                if gene_symbol == '':
                    gene_symbol = gene_synonym
                if gene_symbol == '':
                    gene_symbol = None
                model.addClassToGraph(
                    gene_id, gene_symbol, Genotype.genoparts['gene'])
                if live == 'Dead':
                    model.addDeprecatedClass(gene_id)
                geno.addTaxon(taxon_id, gene_id)
                if gene_synonym != '' and gene_synonym is not None:
                    model.addSynonym(gene_id, gene_synonym)

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

        return

# 需要导入模块: from dipper.models.Model import Model [as 别名]
# 或者: from dipper.models.Model.Model import addDeprecatedClass [as 别名]
    def _process_genes(self, limit=None):

        if self.test_mode:
            graph = self.testgraph
        else:
            graph = self.graph

        geno = Genotype(graph)
        model = Model(graph)

        raw = '/'.join((self.rawdir, self.files['genes']['file']))
        col = self.files['genes']['columns']
        LOG.info("Processing HGNC genes")

        chr_pattern = re.compile(r'(\d+|X|Y|Z|W|MT)[pq$]')
        band_pattern = re.compile(r'([pq][A-H\d]?\d?(?:\.\d+)?)')

        with open(raw, 'r', encoding="utf8") as csvfile:
            filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')

            row = next(filereader)
            if not self.check_fileheader(col, row):
                exit(-1)

            for row in filereader:
                # To generate:
                # head -1 hgnc_complete_set.txt.1 | tr '\t' '\n' |
                # sed "s/\(.*\)/\1 = row[col.index(\'\1\')]/g"

                hgnc_id = row[col.index('hgnc_id')].strip()
                symbol = row[col.index('symbol')].strip()
                name = row[col.index('name')].strip()
                # locus_group = row[col.index('locus_group')]
                locus_type = row[col.index('locus_type')].strip()
                # status = row[col.index('status')]
                location = row[col.index('location')].strip()
                # location_sortable = row[col.index('location_sortable')]
                # alias_symbol = row[col.index('alias_symbol')]
                # alias_name = row[col.index('alias_name')]
                # prev_symbol = row[col.index('prev_symbol')]
                # prev_name = row[col.index('prev_name')]
                # gene_family = row[col.index('gene_family')]
                # gene_family_id = row[col.index('gene_family_id')]
                # date_approved_reserved = row[col.index('date_approved_reserved')]
                # date_symbol_changed = row[col.index('date_symbol_changed')]
                # date_name_changed = row[col.index('date_name_changed')]
                # date_modified = row[col.index('date_modified')]
                entrez_id = row[col.index('entrez_id')].strip()
                ensembl_gene_id = row[col.index('ensembl_gene_id')].strip()
                # vega_id = row[col.index('vega_id')]
                # ucsc_id = row[col.index('ucsc_id')]
                # ena = row[col.index('ena')]
                # refseq_accession = row[col.index('refseq_accession')]
                # ccds_id = row[col.index('ccds_id')]
                # uniprot_ids = row[col.index('uniprot_ids')]
                pubmed_ids = row[col.index('pubmed_id')].strip()  # pipe seperated!
                # mgd_id = row[col.index('mgd_id')]
                # rgd_id = row[col.index('rgd_id')]
                # lsdb = row[col.index('lsdb')]
                # cosmic = row[col.index('cosmic')]
                omim_ids = row[col.index('omim_id')].strip()  # pipe seperated!
                # mirbase = row[col.index('mirbase')]
                # homeodb = row[col.index('homeodb')]
                # snornabase = row[col.index('snornabase')]
                # bioparadigms_slc = row[col.index('bioparadigms_slc')]
                # orphanet = row[col.index('orphanet')]
                # pseudogene.org = row[col.index('pseudogene.org')]
                # horde_id = row[col.index('horde_id')]
                # merops = row[col.index('merops')]
                # imgt = row[col.index('imgt')]
                # iuphar = row[col.index('iuphar')]
                # kznf_gene_catalog = row[col.index('kznf_gene_catalog')]
                # mamit_trnadb = row[col.index('mamit-trnadb')]
                # cd = row[col.index('cd')]
                # lncrnadb = row[col.index('lncrnadb')]
                # enzyme_id = row[col.index('enzyme_id')]
                # intermediate_filament_db = row[col.index('intermediate_filament_db')]
                # rna_central_ids = row[col.index('rna_central_ids')]
                # lncipedia = row[col.index('lncipedia')]
                # gtrnadb = row[col.index('gtrnadb')]

                if self.test_mode and entrez_id != '' and \
                        entrez_id not in self.gene_ids:
                    continue

                if name == '':
                    name = None

                if locus_type == 'withdrawn':
                    model.addDeprecatedClass(hgnc_id)
                else:
                    gene_type_id = self.resolve(locus_type, False)  # withdrawn -> None?
                    if gene_type_id != locus_type:
                        model.addClassToGraph(hgnc_id, symbol, gene_type_id, name)
                    model.makeLeader(hgnc_id)

                if entrez_id != '':
                    model.addEquivalentClass(hgnc_id, 'NCBIGene:' + entrez_id)

                if ensembl_gene_id != '':
#.........这里部分代码省略.........

# 需要导入模块: from dipper.models.Model import Model [as 别名]
# 或者: from dipper.models.Model.Model import addDeprecatedClass [as 别名]
    def _transform_entry(self, e, graph):
        g = graph
        model = Model(g)
        geno = Genotype(graph)

        tax_num = '9606'
        tax_id = 'NCBITaxon:9606'
        tax_label = 'Human'
        build_num = "GRCh38"
        build_id = "NCBIGenome:"+build_num

        # get the numbers, labels, and descriptions
        omimnum = e['entry']['mimNumber']
        titles = e['entry']['titles']
        label = titles['preferredTitle']

        other_labels = []
        if 'alternativeTitles' in titles:
            other_labels += self._get_alt_labels(titles['alternativeTitles'])
        if 'includedTitles' in titles:
            other_labels += self._get_alt_labels(titles['includedTitles'])

        # add synonyms of alternate labels
        # preferredTitle": "PFEIFFER SYNDROME",
        # "alternativeTitles":
        #   "ACROCEPHALOSYNDACTYLY, TYPE V; ACS5;;\nACS V;;\nNOACK SYNDROME",
        # "includedTitles":
        #   "CRANIOFACIAL-SKELETAL-DERMATOLOGIC DYSPLASIA, INCLUDED"

        # remove the abbreviation (comes after the ;) from the preferredTitle,
        # and add it as a synonym
        abbrev = None
        if len(re.split(r';', label)) > 1:
            abbrev = (re.split(r';', label)[1].strip())
        newlabel = self._cleanup_label(label)

        description = self._get_description(e['entry'])
        omimid = 'OMIM:'+str(omimnum)

        if e['entry']['status'] == 'removed':
            model.addDeprecatedClass(omimid)
        else:
            omimtype = self._get_omimtype(e['entry'])
            nodelabel = newlabel
            # this uses our cleaned-up label
            if omimtype == Genotype.genoparts['heritable_phenotypic_marker']:
                if abbrev is not None:
                    nodelabel = abbrev
                # in this special case,
                # make it a disease by not declaring it as a gene/marker
                model.addClassToGraph(omimid, nodelabel, None, newlabel)
            elif omimtype == Genotype.genoparts['gene']:
                if abbrev is not None:
                    nodelabel = abbrev
                model.addClassToGraph(omimid, nodelabel, omimtype, newlabel)
            else:
                model.addClassToGraph(omimid, newlabel, omimtype)

            # add the original screaming-caps OMIM label as a synonym
            model.addSynonym(omimid, label)

            # add the alternate labels and includes as synonyms
            for l in other_labels:
                model.addSynonym(omimid, l, 'OIO:hasRelatedSynonym')

            # for OMIM, we're adding the description as a definition
            model.addDefinition(omimid, description)
            if abbrev is not None:
                model.addSynonym(omimid, abbrev, 'OIO:hasRelatedSynonym')

            # if this is a genetic locus (but not sequenced)
            #   then add the chrom loc info
            # but add it to the ncbi gene identifier,
            # not to the omim id (we reserve the omim id to be the phenotype)
            feature_id = None
            feature_label = None
            if 'geneMapExists' in e['entry'] and e['entry']['geneMapExists']:
                genemap = e['entry']['geneMap']
                is_gene = False

                if omimtype == \
                        Genotype.genoparts['heritable_phenotypic_marker']:
                    # get the ncbigene ids
                    ncbifeature = self._get_mapped_gene_ids(e['entry'], g)
                    if len(ncbifeature) == 1:
                        feature_id = 'NCBIGene:'+str(ncbifeature[0])
                        # add this feature as a cause for the omim disease
                        # TODO SHOULD I EVEN DO THIS HERE?
                        assoc = G2PAssoc(g, self.name, feature_id, omimid)
                        assoc.add_association_to_graph()

                    elif len(ncbifeature) > 1:
                        logger.info(
                            "Its ambiguous when %s maps to >1 gene id: %s",
                            omimid, str(ncbifeature))
                    else:  # no ncbi feature, make an anonymous one
                        feature_id = self._make_anonymous_feature(str(omimnum))
                        feature_label = abbrev

                elif omimtype == Genotype.genoparts['gene']:
#.........这里部分代码省略.........

# 需要导入模块: from dipper.models.Model import Model [as 别名]
# 或者: from dipper.models.Model.Model import addDeprecatedClass [as 别名]
    def _get_gene_history(self, limit):
        """
        Loops through the gene_history file and adds the old gene ids
        as deprecated classes, where the new gene id is the replacement for it.
        The old gene symbol is added as a synonym to the gene.
        :param limit:
        :return:

        """
        if self.testMode:
            g = self.testgraph
        else:
            g = self.graph
        model = Model(g)
        logger.info("Processing Gene records")
        line_counter = 0
        myfile = '/'.join((self.rawdir, self.files['gene_history']['file']))
        logger.info("FILE: %s", myfile)
        with gzip.open(myfile, 'rb') as f:
            for line in f:
                # skip comments
                line = line.decode().strip()
                if re.match(r'^#', line):
                    continue
                (tax_num, gene_num, discontinued_num, discontinued_symbol,
                 discontinued_date) = line.split('\t')

                # set filter=None in init if you don't want to have a filter
                # if self.filter is not None:
                #     if ((self.filter == 'taxids' and \
                #          (int(tax_num) not in self.tax_ids))
                #             or (self.filter == 'geneids' and \
                #                 (int(gene_num) not in self.gene_ids))):
                #         continue
                #  end filter

                if gene_num == '-' or discontinued_num == '-':
                    continue

                if self.testMode and int(gene_num) not in self.gene_ids:
                    continue

                if not self.testMode and int(tax_num) not in self.tax_ids:
                    continue

                line_counter += 1
                gene_id = ':'.join(('NCBIGene', gene_num))
                discontinued_gene_id = ':'.join(('NCBIGene', discontinued_num))

                # add the two genes
                if self.class_or_indiv.get(gene_id) == 'C':
                    model.addClassToGraph(gene_id, None)
                    model.addClassToGraph(
                        discontinued_gene_id, discontinued_symbol)

                    # add the new gene id to replace the old gene id
                    model.addDeprecatedClass(discontinued_gene_id, [gene_id])
                else:
                    model.addIndividualToGraph(gene_id, None)
                    model.addIndividualToGraph(
                        discontinued_gene_id, discontinued_symbol)
                    model.addDeprecatedIndividual(
                        discontinued_gene_id, [gene_id])

                # also add the old symbol as a synonym of the new gene
                model.addSynonym(gene_id, discontinued_symbol)

                if (not self.testMode) and\
                        (limit is not None and line_counter > limit):
                    break

        return

# 需要导入模块: from dipper.models.Model import Model [as 别名]
# 或者: from dipper.models.Model.Model import addDeprecatedClass [as 别名]
    def _process_genes(self, limit=None):

        if self.testMode:
            g = self.testgraph
        else:
            g = self.graph

        geno = Genotype(g)
        model = Model(g)
        raw = '/'.join((self.rawdir, self.files['genes']['file']))
        line_counter = 0
        logger.info("Processing HGNC genes")

        with open(raw, 'r', encoding="utf8") as csvfile:
            filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')
            # curl -s ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt | head -1 | tr '\t' '\n' | grep -n  .
            for row in filereader:
                (hgnc_id,
                 symbol,
                 name,
                 locus_group,
                 locus_type,
                 status,
                 location,
                 location_sortable,
                 alias_symbol,
                 alias_name,
                 prev_symbol,
                 prev_name,
                 gene_family,
                 gene_family_id,
                 date_approved_reserved,
                 date_symbol_changed,
                 date_name_changed,
                 date_modified,
                 entrez_id,
                 ensembl_gene_id,
                 vega_id,
                 ucsc_id,
                 ena,
                 refseq_accession,
                 ccds_id,
                 uniprot_ids,
                 pubmed_id,
                 mgd_id,
                 rgd_id,
                 lsdb,
                 cosmic,
                 omim_id,
                 mirbase,
                 homeodb,
                 snornabase,
                 bioparadigms_slc,
                 orphanet,
                 pseudogene_org,
                 horde_id,
                 merops,
                 imgt,
                 iuphar,
                 kznf_gene_catalog,
                 mamit_trnadb,
                 cd,
                 lncrnadb,
                 enzyme_id,
                 intermediate_filament_db,
                 rna_central_ids) = row

                line_counter += 1

                # skip header
                if line_counter <= 1:
                    continue

                if self.testMode and entrez_id != '' \
                        and int(entrez_id) not in self.gene_ids:
                    continue

                if name == '':
                    name = None
                gene_type_id = self._get_gene_type(locus_type)
                model.addClassToGraph(hgnc_id, symbol, gene_type_id, name)
                if locus_type == 'withdrawn':
                    model.addDeprecatedClass(hgnc_id)
                else:
                    model.makeLeader(hgnc_id)
                if entrez_id != '':
                    model.addEquivalentClass(
                        hgnc_id, 'NCBIGene:' + entrez_id)
                if ensembl_gene_id != '':
                    model.addEquivalentClass(
                        hgnc_id, 'ENSEMBL:' + ensembl_gene_id)
                if omim_id != '' and "|" not in omim_id:
                    omim_curie = 'OMIM:' + omim_id
                    if not DipperUtil.is_omim_disease(omim_curie):
                        model.addEquivalentClass(hgnc_id, omim_curie)

                geno.addTaxon('NCBITaxon:9606', hgnc_id)

                # add pubs as "is about"
                if pubmed_id != '':
#.........这里部分代码省略.........

# 需要导入模块: from dipper.models.Model import Model [as 别名]
# 或者: from dipper.models.Model.Model import addDeprecatedClass [as 别名]
    def _get_gene_history(self, limit):
        """
        Loops through the gene_history file and adds the old gene ids
        as deprecated classes, where the new gene id is the replacement for it.
        The old gene symbol is added as a synonym to the gene.
        :param limit:
        :return:

        """
        src_key = 'gene_history'
        if self.test_mode:
            graph = self.testgraph
        else:
            graph = self.graph
        model = Model(graph)
        LOG.info("Processing Gene records")
        line_counter = 0
        myfile = '/'.join((self.rawdir, self.files[src_key]['file']))
        LOG.info("FILE: %s", myfile)
        col = self.files[src_key]['columns']
        with gzip.open(myfile, 'rb') as tsv:
            row = tsv.readline().decode().strip().split('\t')
            row[0] = row[0][1:]  # strip comment
            if not self.check_fileheader(col, row):
                pass

            for line in tsv:
                # skip comments
                row = line.decode().strip().split('\t')
                if row[0][0] == '#':
                    continue

                tax_num = row[col.index('tax_id')].strip()
                gene_num = row[col.index('GeneID')].strip()
                discontinued_num = row[col.index('Discontinued_GeneID')].strip()
                discontinued_symbol = row[col.index('Discontinued_Symbol')].strip()
                # discontinued_date = row[col.index('Discontinue_Date')]

                # set filter=None in init if you don't want to have a filter
                # if self.id_filter is not None:
                #     if ((self.id_filter == 'taxids' and \
                #          (int(tax_num) not in self.tax_ids))
                #             or (self.id_filter == 'geneids' and \
                #                 (int(gene_num) not in self.gene_ids))):
                #         continue
                #  end filter

                if gene_num == '-' or discontinued_num == '-':
                    continue

                if self.test_mode and gene_num not in self.gene_ids:
                    continue

                if not self.test_mode and tax_num not in self.tax_ids:
                    continue

                line_counter += 1
                gene_id = ':'.join(('NCBIGene', gene_num))
                discontinued_gene_id = ':'.join(('NCBIGene', discontinued_num))
                # add the two genes
                if self.class_or_indiv.get(gene_id) == 'C':
                    model.addClassToGraph(gene_id, None)
                    model.addClassToGraph(discontinued_gene_id, discontinued_symbol)

                    # add the new gene id to replace the old gene id
                    model.addDeprecatedClass(discontinued_gene_id, [gene_id])
                else:
                    model.addIndividualToGraph(gene_id, None)
                    model.addIndividualToGraph(
                        discontinued_gene_id, discontinued_symbol)
                    model.addDeprecatedIndividual(discontinued_gene_id, [gene_id])

                # also add the old symbol as a synonym of the new gene
                model.addSynonym(gene_id, discontinued_symbol)

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