[BioPython] (bio)python for vector cloning

[Leighton Pritchard]

Hi,

On 12/08/2008 13:10, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

>>> What exactly do you mean by plot annotated vector maps?  There are
>>> some basic graphics capabilities in Biopython which use ReportLab.
>>> Depending on what you want to do, GenomeDiagram might be helpful too.
>>> http://bioinf.scri.ac.uk/lp/programs.php#genomediagram
>> 
>> I mean the typical vector graphic representation that gives you an
>> idea of the vector sequence structure (see for instance
>> http://www.addgene.org/pgvec1?f=d&vectorid=345&cmd=genvecmap&dim=800&format=h
>> tml&mtime=1187931178).
>> I would use it for personal documentation, but also when I send the
>> plasmids to other people.
>> 
>> It seems GenomeDiagram could be used for that job, but not without
>> some heavy customization... It would be nice to have something already
>> usable for this purpose.
> 
> I have used GenomeDiagram for plasmid figures, for example showing the
> location of microarray probe target sequences.  However, right now it
> does lack support for "arrowed features" on the circles, and the fancy
> labeling in that example.  So I would agree, recreating that figure
> using Biopython and GenomeDiagram would need plenty of additional
> work.  However, a simplified version would be fairly easy I think.

Peter's correct: currently GenomeDiagram only has support for drawing arrow
features in linear diagrams, and the labelling in the diagram that you link
to is not achievable by the GenomeDiagram API.  Features can be labelled
individually, just not in the style shown.  GenomeDiagram was designed for
the presentation of hundreds of genomes, rather than single plasmids, so
this use is a little out of its original scope ;)

There is a package called Plasmidomics, written in Python, that I've never
used, but which is designed for this kind of task:

http://www.bioprocess.org/plasmid/

It might be what you need and, if the source code is available, you might be
able to work it into your own code.

Cheers,

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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