Fix #169: three-tier protein-coding biotype ontology#357
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Introduces a layered set of flags for "does this transcript make a
polypeptide?":
* `is_protein_coding` - unchanged, strict canonical `protein_coding`
only. Preserves the contract downstream effect predictors (varcode)
depend on.
* `is_protein_coding_extended` - widens to IG/TR gene segments and
translated pseudogenes (`polymorphic_pseudogene`,
`translated_{processed,unprocessed}_pseudogene`). Excludes NMD/NSD
because those products are targeted for degradation rather than
stable accumulation.
* `is_translated` - widest tier. Adds `nonsense_mediated_decay` and
`non_stop_decay` on top of the extended set. Useful when picking the
top variant effect or doing RNA-seq peptide analysis where ribosome
occupancy matters more than stable expression.
Set constants `PROTEIN_CODING_BIOTYPES`,
`EXTENDED_PROTEIN_CODING_BIOTYPES`, and `TRANSLATED_BIOTYPES` are
exposed on `pyensembl.locus_with_genome` so callers can derive their
own categorization if needed.
|
coverage: 85.494% (+0.07%) from 85.426% — fix-169-extended-protein-coding-flags into main |
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Summary
Resolves #169. Adds a layered set of biotype flags for "does this transcript make a polypeptide?":
is_protein_coding— unchanged. Strict canonicalprotein_codingonly. Preserves the contract that downstream effect predictors (e.g. varcode) depend on.is_protein_coding_extended— widens to IG/TR gene segments and translated pseudogenes:IG_{C,D,J,V}_gene,TR_{C,D,J,V}_gene— produce protein after V(D)J recombinationpolymorphic_pseudogene— codes for protein in some individualstranslated_{processed,unprocessed}_pseudogene— pseudogenes with translation evidenceis_translated— widest tier. Addsnonsense_mediated_decayandnon_stop_decayon top. Useful when picking a top variant effect or doing RNA-seq peptide analysis where ribosome occupancy matters more than stable expression.The invariant
strict ⊂ extended ⊂ translatedholds and is tested.The set constants
PROTEIN_CODING_BIOTYPES,EXTENDED_PROTEIN_CODING_BIOTYPES, andTRANSLATED_BIOTYPESare exported frompyensembl.locus_with_genomefor callers who want to derive their own categorization.Test plan
tests/test_extended_protein_coding.pycovers:biotype=Nonepytestpasses locally (56 passed)ruff checkclean