[BioPython] sequence logo with biopython

[bartek wilczynski]

bartek wilczynski <bartek at rezolwenta.eu.org> wrote:

> Giovanni Marco Dall'Olio <dalloliogm at gmail.com> wrote:
> 
> > Hi,
> > is there any way to produce sequence logos[1] with biopython?
> > 
> > I have a set of sequences of the same length, which represent the 5'
> > donorsite in a set of introns.
> > I wonder if there is a way to to create and display a .png logo
> > representation of them, like with this program:
> > - http://weblogo.berkeley.edu/
> > 
> 
> Unfortunately, currently there is no solution in biopython to this. You can
> however take a look at TAMO, a python library designed for working with
> motifs.
> http://fraenkel.mit.edu/TAMO/ I'm not sure if you can make png files with
> it,
> but there are ways to at least obtain text version of the logo.
> 

I've looked into it, and found a way to add this functionality to biopython.

The diff file attached introduces a method .weblogo("filename.png") to the
Bio.AlignAce.Motif class. It is relatively easy to modify the method to be a
standalone function which takes a fasta file as input.

Is it a right time to submit things like this to cvs? I can do that, but I do
not want to mess up the (soon to be available) new release. 

-- 
regards
   Bartek
--
For every complex problem there is an answer that is clear, simple, and wrong. 
                   H. L. Mencken

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