seanome/kmerseek

Get Uniprot domains from overlapping regions found in k-mers

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#6 opened on Feb 11, 2025

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Description

Initial work started in this PR https://github.com/seanome/kmerseek/pull/1 in src/kmerseek/uniprot.py, but it's just a dummy function with pass. Would probably involve JSON and/or XML parsing to search through Uniprot data, but more likely XML because that's the easiest download from the regular Uniprot releases. Also see: https://github.com/olgabot/botryllus-mhc/blob/main/notebooks/400_query_uniprot_rest_api.ipynb

Contributor guide

Research direction
Review the linked PR (#1) and notebook to understand the data format and API. Implement the function in uniprot.py to parse Uniprot XML and extract domains from overlapping k mer regions.
Tech stack
rust
Domain
databioinformatics
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Half day
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Mostly clear
Prerequisites
RustXML parsing
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
40