feat(uniprot): support Ensembl protein accessions in UniProt ID mapping#785
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davereinhart merged 2 commits intoJul 9, 2026
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infer_db_name_from_sequence_accession now recognizes ENSP accessions and maps them to the Ensembl_Protein source, so accession-based target genes with Ensembl protein IDs resolve to a UniProt ID instead of raising NotImplementedError. Also make validate_ensembl_identifier accept versioned Ensembl stable IDs (e.g. ENSP00000369497.3) by stripping the trailing .<version> before the idutils.is_ensembl check, matching how validate_refseq_identifier already handles versioned RefSeq accessions. Related to VariantEffect/dcd_mapping2#110
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davereinhart
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Jul 7, 2026
| If the identifier is not a valid Ensembl identifier. | ||
| """ | ||
| if not idutils.is_ensembl(identifier): | ||
| base_identifier = re.sub(r"\.\d+$", "", identifier) |
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We can remove this line after updating idutils if/when this change gets incorporated:
inveniosoftware/idutils#149
bencap
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Jul 8, 2026
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Extend infer_db_name_from_sequence_accession to recognize ENST identifiers and return "Ensembl_Transcript" as the database name. Restructure control flow to validate each accession type only within its matching branch rather than calling validate_refseq_identifier unconditionally for non-Ensembl accessions.
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infer_db_name_from_sequence_accession now recognizes ENSP accessions and maps them to the Ensembl_Protein source, so accession-based target genes with Ensembl protein IDs resolve to a UniProt ID instead of raising NotImplementedError.
Also make validate_ensembl_identifier accept versioned Ensembl stable IDs (e.g. ENSP00000369497.3) by stripping the trailing . before the idutils.is_ensembl check, matching how validate_refseq_identifier already handles versioned RefSeq accessions.
Related to VariantEffect/dcd_mapping2#110