Python GraphUtils.addDeprecatedClass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 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:
        """
        gu = GraphUtils(curie_map.get())
        if self.testMode:
            g = self.testgraph
        else:
            g = self.graph

        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('^#', 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 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))
                tax_id = ':'.join(('NCBITaxon', tax_num))

                # add the two genes
                gu.addClassToGraph(g, gene_id, None)
                gu.addClassToGraph(g, discontinued_gene_id, discontinued_symbol)

                # add the new gene id to replace the old gene id
                gu.addDeprecatedClass(g, discontinued_gene_id, [gene_id])

                # also add the old symbol as a synonym of the new gene
                gu.addSynonym(g, 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.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils 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

        gu = GraphUtils(curie_map.get())

        logger.info("Processing Gene IDs")
        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) = row
                # 6239,WBGene00000001,aap-1,Y110A7A.10,Live

                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
                gu.addClassToGraph(
                    g, gene_id, gene_symbol, Genotype.genoparts['gene'])
                if live == 'Dead':
                    gu.addDeprecatedClass(g, gene_id)
                geno.addTaxon(taxon_id, gene_id)
                if gene_synonym != '':
                    gu.addSynonym(g, 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.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addDeprecatedClass [as 别名]
    def _process_genes(self, limit=None):
        gu = GraphUtils(curie_map.get())

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

        geno = Genotype(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='\"')
            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) = 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)
                gu.addClassToGraph(g, hgnc_id, symbol, gene_type_id, name)
                if locus_type == 'withdrawn':
                    gu.addDeprecatedClass(g, hgnc_id)
                if entrez_id != '':
                    gu.addEquivalentClass(
                        g, hgnc_id, 'NCBIGene:' + entrez_id)
                if ensembl_gene_id != '':
                    gu.addEquivalentClass(
                        g, hgnc_id, 'ENSEMBL:' + ensembl_gene_id)
                geno.addTaxon('NCBITaxon:9606', hgnc_id)

                # add pubs as "is about"
                if pubmed_id != '':
                    for p in re.split(r'\|', pubmed_id.strip()):
                        if str(p) != '':
                            gu.addTriple(
                                g, 'PMID:' + str(p.strip()),
                                gu.object_properties['is_about'], hgnc_id)

                # add chr location
                # sometimes two are listed, like: 10p11.2 or 17q25
                # -- there are only 2 of these FRA10A and MPFD
                # sometimes listed like "1 not on reference assembly"
                # sometimes listed like 10q24.1-q24.3
                # sometimes like 11q11 alternate reference locus
                band = chrom = None
                chr_pattern = r'(\d+|X|Y|Z|W|MT)[pq$]'
                chr_match = re.match(chr_pattern, location)
                if chr_match is not None and len(chr_match.groups()) > 0:
                    chrom = chr_match.group(1)
                    chrom_id = makeChromID(chrom, 'NCBITaxon:9606', 'CHR')
                    band_pattern = r'([pq][A-H\d]?\d?(?:\.\d+)?)'
                    band_match = re.search(band_pattern, location)
                    f = Feature(hgnc_id, None, None)
                    if band_match is not None and len(band_match.groups()) > 0:
                        band = band_match.group(1)
                        band = chrom + band
                        # add the chr band as the parent to this gene
                        # as a feature but assume that the band is created
                        # as a class with properties elsewhere in Monochrom
                        # TEC Monoch? Monarchdom??
                        band_id = makeChromID(band, 'NCBITaxon:9606', 'CHR')
                        gu.addClassToGraph(g, band_id, None)
                        f.addSubsequenceOfFeature(g, band_id)
                    else:
                        gu.addClassToGraph(g, chrom_id, None)
                        f.addSubsequenceOfFeature(g, chrom_id)

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

            # end loop through file

        gu.loadProperties(g, Feature.object_properties, gu.OBJPROP)
        gu.loadProperties(g, Feature.data_properties, gu.DATAPROP)
        gu.loadProperties(g, Genotype.object_properties, gu.OBJPROP)
        gu.loadAllProperties(g)
#.........这里部分代码省略.........

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

#.........这里部分代码省略.........
            tax_label = 'Human'

            geno.addGenome(tax_id, str(tax_num))   # tax label can get added elsewhere
            gu.addClassToGraph(g, tax_id, None)   # label added elsewhere

            for e in entries:

                # 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(';', label)) > 1:
                    abbrev = (re.split(';', label)[1].strip())
                newlabel = self._cleanup_label(label)

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

                if e['entry']['status'] == 'removed':
                    gu.addDeprecatedClass(g, omimid)
                else:
                    omimtype = self._get_omimtype(e['entry'])
                    # this uses our cleaned-up label
                    gu.addClassToGraph(g, omimid, newlabel, omimtype)

                    # add the original OMIM label as a synonym
                    gu.addSynonym(g, omimid, label)

                    # add the alternate labels and includes as synonyms
                    for l in other_labels:
                        gu.addSynonym(g, omimid, l)

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

                    # if this is a genetic locus (but not sequenced) then add the chrom loc info
                    if omimtype == Genotype.genoparts['biological_region']:
                        if 'geneMapExists' in e['entry'] and e['entry']['geneMapExists']:
                            genemap = e['entry']['geneMap']
                            if 'cytoLocation' in genemap:
                                cytoloc = genemap['cytoLocation']
                                # parse the cytoloc.  add this omim thing as a subsequence of the cytofeature
                                # 18p11.3-p11.2
                                # for now, just take the first one
                                # FIXME add the other end of the range, but not sure how to do that
                                # not sure if saying subsequence of feature is the right relationship
                                cytoloc = cytoloc.split('-')[0]
                                f = Feature(omimid, None, None)
                                if 'chromosome' in genemap:
                                    chrom = makeChromID(str(genemap['chromosome']), tax_num, 'CHR')