sanger-tol/sequencecomposition

Stop codon frequency track

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#26 opened on Jun 17, 2024

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good first issuehelp wanted

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Description

Implement this as a follow-up to fasta_windows, which already count the frequencies of every 3-mer.

We may need to add a parameter to the pipeline to select the right codon table (or add a taxon_id parameter ? is it recorded already in the JSON we get from NCBI datasets ?)

Contributor guide

Research direction
Inspect the existing fasta windows module to understand how 3 mer frequencies are computed. Determine where to add the stop codon frequency track and how to parameterize the codon table. Check if the input JSON from NCBI datasets includes taxon id to automatically select the correct codon table.
Tech stack
groovyshell
Domain
bioinformaticsdata
Issue type
Feature
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.
1-2 days
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
GitNextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60