[Biopython-dev] Enhancements to Bio.Graphics.BasicChromosome

Peter Cock p.j.a.cock at googlemail.com
Mon Oct 3 11:20:21 UTC 2011

Hi Brad (et al),

You might have seen on Twitter at the end of last week I mentioned
some work to extend Brad's Bio.Graphics.BasicChromosome to allow
features within a chromosome segment, optionally with labels.

The branch is here:

I put together a non-trivial example of showing the tRNA genes in
Arabidopsis as a unit test in test_GraphicsChromosome.py - this is
deliberately showing too many features in order to check the label
placement algorithm:


This kind of figure is also used for showing SNP placement and genetic
marker loci used in breeding etc.

If I had put more (or a more uniform set of) features you'd get
something worthy of the nickname "millipede diagram", looking like a
segmented body (the chromosome) with thousands of legs (the lines for
the labels).

This isn't quite backwards compatible - the old code draws the
chromosomes left aligned within their allocated space, while I put
them centrally in order to draw labels on either side.

Iddo sounded enthusiastic on Twitter. Does this look worth including
as is? Would someone (doesn't have to be Brad) like to test/review it



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