obophenotype / obophenotype/ncbitaxon
Enhance Python code for subset extraction
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- Dominant language
- Python
- Stars
- 31
- Forks
- 7
- PR merge metrics
- No merged PRs in 30d
Description
The current code in #30 can be configured to generate only classes with a given set of tax_ids. By adding one more pass through nodes.dmp we could find all the ancestors of a given set of tax_ids, then generate a subset from that. I expect that would be more efficient than extracting from .obo like this https://github.com/obophenotype/ncbitaxon/blob/master/subsets/Makefile#L8
Contributor guide
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 implementation from issue #30 and the existing subset extraction workflow. Trace how nodes.dmp represents parent relationships, then compare the proposed approach with the .obo extraction in the linked Makefile. Done means configured tax_ids produce a subset containing their ancestors without relying on .obo parsing.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100