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<div class="">Hi Spencer,</div>
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<div class="">On 26 Apr 2017, at 15:01, Spencer Bliven <<a href="mailto:spencer.bliven@gmail.com" class="">spencer.bliven@gmail.com</a>> wrote:</div>
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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
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<div>There aren’t any, I’m afraid…</div>
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It would also be nice to have some user interaction (zooming, toggling tracks, etc), e.g. as a jupyter widget.</div>
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<div>I would agree ;)</div>
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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.
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<div>I agree - we offered up a GSoC project to do this a while back, but it didn’t come off, in the end.</div>
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<div>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…</div>
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There appears to be a project based off BioJulia to display the Dalliance browser (<a href="https://github.com/BioJulia/Dalliance.jl/blob/master/src/Dalliance.jl" class="">https://github.com/BioJulia/Dalliance.jl/blob/master/src/Dalliance.jl</a>), 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?</div>
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<div>I’m not aware of any, I’m afraid.</div>
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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?</div>
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<div>I’d certainly be interested in that. A SeqRecord.draw() method with suitable options would be very nice, for instance.</div>
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<div>I’m all for a complete overhaul/replacement of GenomeDiagram, especially if others are up for the challenge :D</div>
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<div>Cheers,</div>
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<div>L.</div>
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--<br class="">
Dr Leighton Pritchard<br class="">
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme<br class="">
DG31, James Hutton Institute (Dundee)<br class="">
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA<br class="">
e: <a href="mailto:leighton.pritchard@hutton.ac.uk" class="">leighton.pritchard@hutton.ac.uk</a> w:
<a href="http://www.hutton.ac.uk/staff/leighton-pritchard" class="">http://www.hutton.ac.uk/staff/leighton-pritchard</a><br class="">
gpg/pgp: 0xFEFC205C tel: +44(0)844 928 5428 x8827 or +44(0)1382 568827<br class="">
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