VariantEffect / dcd_mapping2

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Build Type

push

github

Committed by bencap

Commit Message

feat(transcripts): map non-RefSeq accession targets to RefSeq MANE counterparts

Accession-based targets declared with Ensembl protein (ENSP) or transcript
(ENST) accessions previously passed through as bare, unresolved accessions or
were dropped, leaving downstream annotation inconsistent with the RefSeq
accessions used elsewhere in the pipeline. Resolving them to their RefSeq MANE
counterpart keeps output consistent regardless of how the target was declared.

- add get_gene_symbol_from_ensembl_protein / _transcript lookups as the bridge
  from a non-RefSeq accession to get_mane_transcripts_for_gene
- add _select_refseq_protein_counterpart / _select_refseq_cdna_counterpart,
  falling back to the bare accession (protein) or None (cDNA, since np is
  required on TxSelectResult) when no counterpart resolves
- skip standalone VRS mapping for a target with no record group of its own
  (e.g. base-editor score sets where every row groups under the cDNA target)
  instead of KeyError'ing on records[target_gene]
- re-raise the original alignment error instead of losing its traceback via
  `raise AlignmentError from e`

Coverage Stats

0 of 33 new or added lines in 5 files covered. (0.0%)

5 existing lines in 4 files now uncovered.

0 of 3146 relevant lines covered (0.0%)

0.0 hits per line