cancervariants / cancervariants/gene-normalization
NCBI importer creates redundant records for some genes
Open
bug
priority:low
- Dominant language
- Python
- Stars
- 3
- Forks
- 4
- PR merge metrics
- No merged PRs in 30d
Description
full list here: https://gist.github.com/jsstevenson/fba1e6c33e438c9018c1ec43a0ea6ba7
Looks like it happens between genes created in `_get_gene_info()` and `_get_gene_gff()`. Using concept ID (instead of symbol) as a key on line 265 of the importer might fix this.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with the importer around line 265 and trace how _get_gene_info() and _get_gene_gff() create records. Use the linked gist to reproduce the redundant gene records and verify that processing the listed genes no longer creates duplicates.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100