cancervariants / cancervariants/variation-normalization
gnomad_vcf_to_protein warnings for intron variants
- Dominant language
- Python
- Stars
- 15
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
`variation/gnomad_vcf_to_protein?q=7-55142262-G-A` returns `Unable to get transcripts given NC_000007.14 and 55142262` in its warnings. This is because it maps to a location on an intron rather than an exon. It'd be more useful to have the warnings contain a message saying that it's unable to translate to protein variation since it's an intron variant
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by calling the variation/gnomad_vcf_to_protein endpoint with q=7-55142262-G-A and trace where its warnings are assembled. Update the warning for an intron mapping to state that the variant cannot be translated to a protein variation, then verify that this input produces the clearer message.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100