[BioPython] sequence logo with biopython

[bartek wilczynski]

Peter <biopython at maubp.freeserve.co.uk> wrote:

> > 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. 
> 
> Its a very small change, but lets see what Michiel says for the timing.
> 
It is indeed a very small change, however it seems to have at least one
prospective user ;). Also it is almost impossible to break anything by
including it in the new release. 

> It might be nice to expose all the options to the end user, possibly as 
> handled in the Bio/Blast/NCBIWWW.py qblast() function, or using **keywds 
> as in Bio/Blast/NCBIStandalone.py  blastall() etc.

Good idea, I've included a new diff, which allows for passing any keys directly
from function call to the weblogo server such as:

m.weblogo("x.png",colorscheme="BW") # brings you a monochrome logo image

BTW. It would be interesting to know if there are more people interested in
using a better module for sequence motifs. I have some code lying arround and
some ideas on how it could be put together, but since there were no documented
cases of anyone using Bio.AlignAce or Bio.MEME, I'm not sure if it's worth the
extra work.

-- 
cheers
   Bartek

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