Consolidate ORF/RNA dependencies and adopt Biotite for independent sequence checks
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Refactor
- Clarity
- Mostly clear
- Activity status
- Active
- Domain
- backend, bioinformatics
Research direction
Start with pyproject.toml, varcode/effects/translate.py, and varcode/effects/codon_tables.py, then read coordination issue #6 and the linked pandas work in #612. Run the existing translation and codon-table tests to establish the current behavior before evaluating Biotite against the listed edge cases. Done means normal-install smoke tests, regression suites, and pip check pass, with source or output differences and retained runtime extras explained.
Written by the indexing model from the issue text.
Description
Coordination: https://github.com/openvax/openvax2/issues/6
Current metadata has orf and uorf aliases installing Orfdata/PyEnsembl, rna for pysam, and test-data for Osteosarc/Biopython. Requirements still permit pandas 2.2.2. Translation/codon-table code has deliberately removed runtime Biopython and encodes variant-specific semantics.
- Consolidate common ORF/RNA capabilities into normal dependencies, preserving explicit downloadable test data. Reuse #612 for pandas 3+.
- Replace Bio-based independent checks with Biotite; audit duplicated generic sequence primitives for justified reuse, without replacing Varcode consequence semantics or changing emitted hypotheses.
- Cover every supported NCBI codon table, alternative starts, mitochondrial exceptions, ambiguity, stops, frameshifts, partial transcripts and unresolved/SV alternatives. Do not silently substitute Biotite defaults for the established contract.
- Check potential dependency cycles and release Orfdata/PyEnsembl foundations before consumers. Ordinary
pip install varcodeshould support the agreed common capabilities.
Sources: metadata, translation, codon tables.
Acceptance: normal-install smoke tests, relevant regression suites and pip check pass; source/output differences and any retained runtime extras have explicit reasons. Published compatible versions and editable local work are preserved. This issue requests implementation, not an unverified dependency substitution.
Documentation consistency found during the 2026-10-27 audit
The stale ORFdata 0.34/0.35 installation claims were corrected in PR #654, released as Varcode 10.22.2. The guide now matches orfdata[pyensembl]>=0.39.0,<1 in package metadata. Dependency consolidation and the other acceptance criteria above remain open; this documentation correction does not implement them.
- Dominant language
- Python
- Stars
- 88
- Forks
- 28
- Avg merge
- 3h 10m
- Merged PRs (30d)
- 53
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