ProteinBot.py 文件源码

def make_gene_encodes(self, write=True):
        """
        Add an "encodes" statement to the gene item
        :return:
        """
        uniprot_ref = make_ref_source(self.record['uniprot']['@source'], PROPS['UniProt ID'],
                                      self.external_ids['UniProt ID'],
                                      login=self.login)

        try:
            statements = [wdi_core.WDItemID(self.protein_wdid, PROPS['encodes'], references=[uniprot_ref])]
            wd_item_gene = wdi_core.WDItemEngine(wd_item_id=self.gene_wdid, domain='genes', data=statements,
                                                 append_value=[PROPS['encodes']], fast_run=fast_run,
                                                 fast_run_base_filter={PROPS['Entrez Gene ID']: '',
                                                                       PROPS['found in taxon']: self.organism_info[
                                                                           'wdid']},
                                                 global_ref_mode="CUSTOM", ref_handler=update_retrieved_if_new)
            wdi_helpers.try_write(wd_item_gene, self.external_ids['UniProt ID'], PROPS['UniProt ID'], self.login,
                                  write=write)
        except Exception as e:
            exc_info = sys.exc_info()
            traceback.print_exception(*exc_info)
            msg = wdi_helpers.format_msg(self.external_ids['UniProt ID'], PROPS['UniProt ID'], None,
                                         str(e), msg_type=type(e))
            wdi_core.WDItemEngine.log("ERROR", msg)