[Biopython-dev] Bio.Graphics and GenomeDiagram

Leighton Pritchard lpritc at scri.ac.uk
Thu Oct 16 09:17:57 UTC 2008

On 15/10/2008 18:32, "Robert Cadena" <robert.cadena at gmail.com> wrote:

> I'd been working on and off on writing clones of bioperl's and
> bioruby's graphics libraries:
> http://www.bioperl.org/wiki/HOWTO:Graphics
> http://bio-graphics.rubyforge.org/


> maybe there's the possibility of incorporating the bit of code I have
> to create a bioperl::graphics library clone.

I would see GenomeDiagram as existing alongside a Bioperl::Graphics clone,
providing extra functionality that (for now) is not present in
Bioperl/Bioruby, so I don't see our approaches clashing on that level.

> I'd be happy to volunteer some time to help with GenomeDiagram

Thanks Robert, that's very welcome.  The way I would like to move forward is
to branch code off from the current version of GenomeDiagram, to make it
work as though it's part of Biopython (sitting under Bio.Graphics), then
neaten up the internals, add unit tests and documentation, before adding
enhancement features/fixing a couple of outstanding issues.  You can get a
copy of the current GenomeDiagram code and documentation at
http://bioinf.scri.ac.uk/lp/programs.php, and I'm happy to field design
questions/comments either here or off-list.

Initially I had thought to handle the first stages of this (up to and
including neatening internals) myself before seeking code inclusion in
Biopython, as I have an informal plan for what needs to be done, already.
I'm open to advice and suggestions - including "I can do all that, if you
like" - though ;)



Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
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