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Test Ensembl transcripts without gene features - #8

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byee4 merged 1 commit into
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tests/issue-3-ensembl-gtf
Oct 5, 2026
Merged

byee4 merged 1 commit into
masterfrom
tests/issue-3-ensembl-gtf

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@byee4 byee4 commented Oct 5, 2026

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Summary

  • Add a small Ensembl-format GTF, matching gffutils SQLite database, and BED example without gene rows.
  • Include a curated record for ENST00000606034, the transcript named in issue annotator does not always annotate using Ensembl (and 10X) GTF files #3.
  • Verify the committed database matches a rebuild and produces coding, UTR, intergenic, and noncoding annotations.

Verification

  • python -m pytest -q unit_tests — 8 passed.

Issue status

Related to #3. The missing-gene case now annotates correctly in this regression fixture, including the named transcript ID. The complete Ensembl release 87 file was not part of the report's reproduction data, so this PR documents and tests the behavior without changing production code.

@byee4
byee4 merged commit 7f138ce into master Oct 5, 2026
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