[BioPython] sequence logo with biopython

[bartek wilczynski]

Giovanni Marco Dall'Olio <dalloliogm at gmail.com> wrote:

> 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

Well, the quick answer is that it is the most convenient place for me to put it.
Since there is a Motif class for sequence motif objects, it is not a bad one. 

A longer answer is that biopython does not have a good infrastructure for
dealing with motifs. I've contributed the AlignAce lib, Jason Hackney
contributed the MEME library, which includes another Motif class, very similar,
but not exactly compatible with AlignAce code. 

I planned once to do some refactoring work to unify these to modules, but so far
did not find the time to do it. Now, since there is TAMO library available ,
there is even less incentive to do so (even though I do not use  TAMO myself).

cheers bartek