Plot sequence differences from reference
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
We want two new plots that show significant differences between the sample sequence and a reference sequence. One plot will be in base space and one in amino acid space.
We could have the sequence coordinates along the X axis, and then show the percentage of variance along the Y axis. We would only plot variants that exceeded some threshold to avoid cluttering the plot. For example, only show variants that exceed 2% of the reads. If one position has more than one variant exceeding the threshold, plot them as stacked bars. Each bar is labelled with a letter to show the base or acid present.
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
The issue does not name files, tests, or an entry point. Start by locating the sequence-comparison and plotting code, then trace how reference-relative base and amino acid variants are represented. Done means adding both thresholded plots, including stacked labels for multiple variants at one position, with tests or example output that verify the requested behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100