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src/b/i/biopython-1.63/Bio/SeqIO/UniprotIO.py   biopython(Download)
        def _parse_name(element):
            self.ParsedSeqRecord.name = element.text
            self.ParsedSeqRecord.dbxrefs.append(self.dbname + ':' + element.text)
 
        def _parse_accession(element):
            append_to_annotations('accessions', element.text)  # to cope with SwissProt plain text parser
            self.ParsedSeqRecord.dbxrefs.append(self.dbname + ':' + element.text)
                            append_to_annotations("organism_name", organism_element.text)
                elif organism_element.tag == NS + 'dbReference':
                    self.ParsedSeqRecord.dbxrefs.append(organism_element.attrib['type'] + ':' + organism_element.attrib['id'])
                elif organism_element.tag == NS + 'lineage':
                    for taxon_element in organism_element:
        def _parse_dbReference(element):
            self.ParsedSeqRecord.dbxrefs.append(element.attrib['type'] + ':' + element.attrib['id'])
            #e.g.
            # <dbReference type="PDB" key="11" id="2GEZ">
            #   <property value="X-ray" type="method"/>
                                authors.append(person_element.attrib['name'])
                        elif cit_element.tag == NS + 'dbReference':
                            self.ParsedSeqRecord.dbxrefs.append(cit_element.attrib['type']
                                                                + ':' + cit_element.attrib['id'])
                            if cit_element.attrib['type'] == 'PubMed':

src/b/i/biopython-HEAD/Bio/SeqIO/UniprotIO.py   biopython(Download)
        def _parse_name(element):
            self.ParsedSeqRecord.name = element.text
            self.ParsedSeqRecord.dbxrefs.append(self.dbname + ':' + element.text)
 
        def _parse_accession(element):
            append_to_annotations('accessions', element.text)  # to cope with SwissProt plain text parser
            self.ParsedSeqRecord.dbxrefs.append(self.dbname + ':' + element.text)
                            append_to_annotations("organism_name", organism_element.text)
                elif organism_element.tag == NS + 'dbReference':
                    self.ParsedSeqRecord.dbxrefs.append(organism_element.attrib['type'] + ':' + organism_element.attrib['id'])
                elif organism_element.tag == NS + 'lineage':
                    for taxon_element in organism_element:
        def _parse_dbReference(element):
            self.ParsedSeqRecord.dbxrefs.append(element.attrib['type'] + ':' + element.attrib['id'])
            #e.g.
            # <dbReference type="PDB" key="11" id="2GEZ">
            #   <property value="X-ray" type="method"/>
                                authors.append(person_element.attrib['name'])
                        elif cit_element.tag == NS + 'dbReference':
                            self.ParsedSeqRecord.dbxrefs.append(cit_element.attrib['type']
                                                                + ':' + cit_element.attrib['id'])
                            if cit_element.attrib['type'] == 'PubMed':

src/b/i/biopython-1.63/Bio/SeqIO/SwissIO.py   biopython(Download)
            dbxref = "%s:%s" % (database, accession)
            if not dbxref in record.dbxrefs:
                record.dbxrefs.append(dbxref)
        annotations = record.annotations
        annotations['accessions'] = swiss_record.accessions

src/b/i/biopython-1.63/Bio/GenBank/Scanner.py   biopython(Download)
                        elif qualifier_name == "db_xref":
                            #its a list, possibly empty.  Its safe to extend
                            record.dbxrefs.append(qualifier_data)
                        else:
                            if qualifier_data is not None:

src/b/i/biopython-HEAD/Bio/SeqIO/SwissIO.py   biopython(Download)
            dbxref = "%s:%s" % (database, accession)
            if not dbxref in record.dbxrefs:
                record.dbxrefs.append(dbxref)
        annotations = record.annotations
        annotations['accessions'] = swiss_record.accessions

src/b/i/biopython-HEAD/Bio/GenBank/Scanner.py   biopython(Download)
                        elif qualifier_name == "db_xref":
                            #its a list, possibly empty.  Its safe to extend
                            record.dbxrefs.append(qualifier_data)
                        else:
                            if qualifier_data is not None: