[Biopython] Genome browser for BioPython annotations

[Leighton Pritchard]

Hi Spencer,

On 26 Apr 2017, at 15:01, Spencer Bliven <spencer.bliven at gmail.com<mailto: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)
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e: leighton.pritchard at hutton.ac.uk<mailto:leighton.pritchard at hutton.ac.uk>       w: http://www.hutton.ac.uk/staff/leighton-pritchard
gpg/pgp: 0xFEFC205C tel: +44(0)844 928 5428 x8827 or +44(0)1382 568827


The James Hutton Institute is a Scottish charitable company limited by guarantee.
Registered in Scotland No. SC374831
Registered Office: The James Hutton Institute, Invergowrie Dundee DD2 5DA.
Charity No. SC041796
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170426/75851746/attachment.html>