openvax / pyensembl

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Build # 25749148193

Build Type

push

github

Committed by web-flow

Commit Message

Fix #242: expose Ensembl annotation versions on Gene/Transcript/Exon/Protein (#341)

The transcript_version, gene_version, exon_version, and protein_version
columns were already loaded into the sqlite database from modern Ensembl
GTFs; they were just never surfaced on the Python objects.

Each entity now has a prefixed canonical accessor and a generic alias:

  Gene       gene_version       / versioned_gene_id
              version            / versioned_id  (aliases)

  Transcript transcript_version / versioned_transcript_id
              version            / versioned_id  (aliases)
              protein            -> new Protein view (or None for noncoding)

  Exon       exon_version       / versioned_exon_id
              version            / versioned_id  (aliases)
              exon_version is now a constructor kwarg (default None)

  Protein    protein_id, protein_version (primary)
              id, version, versioned_protein_id, versioned_id (aliases)

All version accessors return None when the GTF omits the corresponding
attribute (e.g. TAIR), and versioned_id falls back to the unversioned id
in that case.

Bump version to 2.7.0.

Coverage Stats

92 of 101 new or added lines in 7 files covered. (91.09%)

1463 of 1739 relevant lines covered (84.13%)

3.37 hits per line