[Biopython-dev] ColorSpiral for Bio.Graphics

Peter Cock p.j.a.cock at googlemail.com
Mon Sep 24 08:53:07 UTC 2012

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:

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:

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:

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):



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