diff --git a/kg_covid_19/transform_utils/string_ppi/string_ppi.py b/kg_covid_19/transform_utils/string_ppi/string_ppi.py index 42f511d2..fdaffb52 100644 --- a/kg_covid_19/transform_utils/string_ppi/string_ppi.py +++ b/kg_covid_19/transform_utils/string_ppi/string_ppi.py @@ -157,7 +157,6 @@ def run(self, data_file: Optional[str] = None) -> None: for protein_name in ('protein1', 'protein2'): protein = get_item_by_priority(items_dict, [protein_name]) protein = '.'.join(protein.split('.')[1:]) - protein = f"ENSEMBL:{protein}" proteins.append(protein) if protein in self.protein_gene_map: gene = self.protein_gene_map[protein] @@ -182,7 +181,7 @@ def run(self, data_file: Optional[str] = None) -> None: data=[ ensemble_gene, "biolink:has_gene_product", - protein, + f"ENSEMBL:{protein}", "RO:0002205", "NCBI", ] + extra_header @@ -202,7 +201,7 @@ def run(self, data_file: Optional[str] = None) -> None: write_node_edge_item( fh=edge, header=self.edge_header, - data=[proteins[0], edge_label, proteins[1], + data=[f"ENSEMBL:{proteins[0]}", edge_label, f"ENSEMBL:{proteins[1]}", relation, "STRING", items_dict['combined_score']] + [ items_dict.get(header, "") for header in edge_additional_headers