[Biopython] Genome browser for BioPython annotations

Spencer Bliven spencer.bliven at gmail.com
Fri Apr 28 11:11:54 UTC 2017


Thanks Leighton. That was more or less what I was expecting. I probably won't be able to do a complete overhaul at this point, but I'll keep it in mind e.g. as a potential student project.

-Spencer

On April 26, 2017 at 17:18:31, Leighton Pritchard (leighton.pritchard at hutton.ac.uk) wrote:

Hi Spencer,

On 26 Apr 2017, at 15:01, Spencer Bliven <spencer.bliven at gmail.com> wrote:

I'm trying to compare sequence annotations from a few sources. I'm currently displaying the annotations as different tracks in a GenomeDiagram. However, I occasionally need single-base resolution, and I'm not aware of any options in GenomeDiagram for displaying the sequence.

There aren’t any, I’m afraid…

It would also be nice to have some user interaction (zooming, toggling tracks, etc), e.g. as a jupyter widget.

I would agree ;)

My ideal would be a html/javascript genome browser that had been wrapped up as a jupyter widget and would accept SeqRecord objects as the datasource and display any SeqFeatures.

I agree - we offered up a GSoC project to do this a while back, but it didn’t come off, in the end.

Doing this would benefit from a complete overhaul (i.e. rewriting) of the backend. I’ve got some ideas for this, but not a lot of time to implement…

There appears to be a project based off BioJulia to display the Dalliance browser (https://github.com/BioJulia/Dalliance.jl/blob/master/src/Dalliance.jl), but dalliance isn't really suited for light-weight visualization. Is anyone aware of similar projects for BioPython? Are there other tools that might be useful in visualizing the positions of SeqFeatures at a detailed level?

I’m not aware of any, I’m afraid.

BTW, I was a bit surprised at how much code it took to add BioPython objects to a GenomeDiagram. No doubt this is due to the package history. Would there be interest in tighter integration of GenomeDiagram into BioPython?

I’d certainly be interested in that. A SeqRecord.draw() method with suitable options would be very nice, for instance.

I’m all for a complete overhaul/replacement of GenomeDiagram, especially if others are up for the challenge :D

Cheers,

L.

--
Dr Leighton Pritchard
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme
DG31, James Hutton Institute (Dundee)
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