cancervariants / cancervariants/gene-normalization
Store HGNC locations as sequence location
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 3
- Forks
- 4
- PR merge metrics
- No merged PRs in 30d
Description
We can look at the VRS-Python related code for how to do this: https://github.com/ga4gh/vrs-python/blob/main/src/ga4gh/vrs/extras/localizer.py . We may want to wait until this related issue is resolved.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the VRS-Python localizer.py implementation linked in the issue and inspect related issue #268 before deciding on an approach. Trace how HGNC locations are currently represented in gene-normalization. Done means HGNC locations are stored as sequence locations, with behavior aligned to the relevant VRS-Python guidance.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100