Miladeb77/Y2_Genepanel_project

Ensembl Optimisation

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#9 opened on Dec 10, 2024

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backendenhancementhelp wantedsprint3

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Description

Trello: https://trello.com/b/WAMAUQjB/stp-year2-software-eng-project The api_ensembl code takes the ENSG IDs from panelgenemapper and uses it as input for an api request which will retrieve the bed file for all the exons within the genes in the specified panel.

For R-code 58 it has 123 genes and takes 4 minutes and 46 seconds to run - Need help trying to optimize timings for this.

Contributor guide

Research direction
Profile the current script to identify bottlenecks, explore batching Ensembl REST API requests, consider caching responses locally, and use parallel requests where possible.
Tech stack
python
Domain
backendapi
Issue type
Performance
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
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.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Mostly clear
Prerequisites
GitPythonREST API
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
65