diff --git a/README.md b/README.md index 4089a2a..abb7925 100644 --- a/README.md +++ b/README.md @@ -264,8 +264,6 @@ The project is: _in progress_. ## Room for Improvement Room for improvement: - Better tests -- Try incorporating unipressed -- Improve overlap computations To do: - Support for more species diff --git a/src/sponge/modules/ppi_retriever/ppi_retriever.py b/src/sponge/modules/ppi_retriever/ppi_retriever.py index 607ffe7..e817c20 100644 --- a/src/sponge/modules/ppi_retriever/ppi_retriever.py +++ b/src/sponge/modules/ppi_retriever/ppi_retriever.py @@ -108,7 +108,7 @@ def retrieve_ppi( print ('Checking the conflicts in the UniProt database...') mapper = ProteinIDMapper(self.protein_url) uniprot_df = mapper.get_uniprot_mapping('Gene_Name', 'UniProtKB', - ids_to_check).set_index('from') + ids_to_check, taxonomy_id=9606).set_index('from') p_to_q = {p: q for q,p in zip(diff_df['queryName'], diff_df['preferredName'])} # Keep the conflicts where there is a match or where one or both