[Biopython-dev] Cross-links between tracks in GenomeDiagram

Peter Cock p.j.a.cock at googlemail.com
Thu Nov 17 15:10:34 UTC 2011

On Thu, Nov 17, 2011 at 12:24 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Nov 17, 2011 at 11:51 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> Peter;
>>> Something I've been working on this month in discussion with Leighton
>>> is some enhancements to GenomeDiagram, driven partly by a figure
>>> I wanted to draw for a paper. The code is here,
>>> https://github.com/peterjc/biopython/tree/gd-links
>> Awesome. The direction you are pushing this is great. I'd definitely
>> love to see this in the next release.
> Cool. It will end up being a graphics heavy release at this rate :)

Committed to trunk,

>>> Also try the file Doc/example/ACT_example.py which mimics
>>> a simple two-reference ACT diagram:
>>> https://github.com/peterjc/biopython/blob/gd-links/Doc/examples/ACT_example.py
>>> Simple linear output (split into three fragments) shown here:
>>> http://twitter.com/#!/pjacock/status/136509137826754560
>> Really nice. My only suggestion would be to combine the examples and
>> outputs together in the Cookbook. One of the best ways to learn plotting
>> and drawing packages is by looking through examples, finding one that
>> most closely matches what you want, and then iterating until you get at
>> what you need.
> Unless I can find a nicer small sample dataset (or make one) which
> includes an inversion, I plan to use that ACT sample data in the
> tutorial - basically taking the user though the ACT_example.py
> script.

I plan to do another OBF blog entry on this as well, probably
with the same example.


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