[BioPython] sequence logo with biopython

[Giovanni Marco Dall'Olio]

Thank you: this is very good.

I see that it uses the berkeley weblogo website and urllib.

just one newbie question: why do you put it in the Bio.AlignAce.Motif class?
Thanks

Giovanni

2007/9/17, bartek wilczynski <bartek at rezolwenta.eu.org>:
> 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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