Miladeb77/Y2_Genepanel_project

Bed file integration

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#3 opened on Nov 20, 2024

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Description

Issue:

I have managed to extract the gene name start, end and chromosome from ensembl api. However, I am having trouble figuring out how to convert this to a bed file with all the transcripts for the gene

Contributor guide

Research direction
Investigate how to use the Ensembl REST API to fetch all transcripts for a gene, and understand the BED file format. Then explore how to map the gene coordinates to transcript coordinates and generate a BED file in Python.
Tech stack
python
Domain
data
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.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Mostly clear
Prerequisites
Git
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
65