[Biopython-dev] ColorSpiral for Bio.Graphics

Peter Cock p.j.a.cock at googlemail.com
Thu Sep 27 13:01:44 UTC 2012

On Mon, Sep 24, 2012 at 9:53 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hello all,
> Last week Leighton was doing some work with Biopython
> and GenomeDiagram using the cross-links functionality
> we worked on for Biopython 1.59, which I described here:
> http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/
> As you may have noticed via Twitter or his blog, Leighton has
> generated an enormous (5m by 1m) PDF poster printout
> comparing 29 bacterial genomes:
> http://armchairbiology.blogspot.co.uk/2012/09/the-colours-man-colours.html
> As he describes on his blog post, this required generating
> arbitrary color sets, with the option of adding some noise
> (or jitter as he called it) to make neighbouring colours
> visually distinct (rather than the more typical requirement
> of a smooth value to color mapping).
> His code to do that is now on this branch (with a minor
> bug fix and a few more docstrings added), ready for
> possible merging into Biopython:
> https://github.com/peterjc/biopython/tree/colorspiral
> Does this seem like a sensible addition to Bio.Graphics?
> Does anyone have any thoughts on the namespace
> Bio.Graphics.ColorSpiral given it defines an object
> ColorSpiral? Might a Bio.Graphics.Colors be useful?
> (If as discussed on the other thread we move to lower
> case module names for Python 3, this namespace
> clash also present in many other Biopython modules
> goes away):
> http://lists.open-bio.org/pipermail/biopython-dev/2012-September/009934.html
> Regards,
> Peter

I've committed it - we can still move/rename/etc until the
next release if anyone has suggestions for improvement.


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