[Biopython-dev] Bio.Graphics and GenomeDiagram

[Leighton Pritchard]

Hi,

A while ago I wrote the GenomeDiagram library for drawing images of genomes
and other large biological sequences, and collections of sequences
(http://bioinf.scri.ac.uk/lp/programs.php#genomediagram).  This library
already uses Biopython objects (Seq, SeqFeature, etc.) and, like other
modules in Bio.Graphics, has a dependency on Reportlab only.  It's been
published, and has found use in other groups, who seem to be using it
without any issues - there's been a trickle of maintenance requests, but
nothing of late other than questions from people new to Python.

Now that I have managed to free up a little bit of time I'd like to revisit
GenomeDiagram, tidy up the internals some more (there's some clunky stuff in
there...), and contribute it to Bio.Graphics - which hasn't seen much
traffic for a while.  Looking at the current Bio.Graphics structure, I think
that incorporating the (revised) library as Bio.Graphics.GenomeDiagram in a
directory under Bio.Graphics would be a suitable approach.  I'm happy to
maintain this code for the foreseeable future, also - though help is, of
course, welcome.  There is written documentation, which I would happily move
over to the wiki, and some testing in __name__ == '__main__', which could be
expanded upon and moved over to a unit test format for consistency.

One of the things I would like to do to expand on current functionality is
to provide some library methods that produce commonly-desired output,
similar to that in GenomeAtlas
(http://www.cbs.dtu.dk/services/GenomeAtlas/), so that users don't have to
know about the internals of GenomeDiagram, and something like a
Bio.Graphics.GenomeDiagram.draw_seqrecord_cds(style='circular',
gc_content=True, outfile='cds1.pdf') call would produce a simple circular
diagram of CDS features with accompanying graph of GC content.

I suggested something doing similar a while ago and got no feedback - does
anyone object to this contribution, in principle or in practice?  Or are
there any other comments?  I'm all (well, mostly) ears...

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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