<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Thanks <span style="font-family: Helvetica; font-size: 14px;">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.</span><br style="font-family: Helvetica; font-size: 14px;"></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><span style="font-family: Helvetica; font-size: 14px;"><br></span></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><span style="font-family: Helvetica; font-size: 14px;">-Spencer</span></div> <div id="bloop_sign_1493377719260537088" class="bloop_sign"></div> <br><p class="airmail_on">On April 26, 2017 at 17:18:31, Leighton Pritchard (<a href="mailto:leighton.pritchard@hutton.ac.uk">leighton.pritchard@hutton.ac.uk</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div></div><div>
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<div class="">Hi Spencer,</div>
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<blockquote type="cite" class="">
<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>
<br class="Apple-interchange-newline">
<div class="">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">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.</div>
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<div>There aren’t any, I’m afraid…</div>
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<blockquote type="cite" class="">
<div class="">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">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>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">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.</div>
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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>
<br class="">
<blockquote type="cite" class="">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">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>
<br class="">
<blockquote type="cite" class="">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">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>
<div><br class=""></div>
<div>L.</div>
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<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;">--<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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<br>
<p>The James Hutton Institute is a Scottish charitable company
limited by guarantee.<br>
Registered in Scotland No. SC374831<br>
Registered Office: The James Hutton Institute, Invergowrie Dundee
DD2 5DA.<br>
Charity No. SC041796</p>
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