[BioPython] sequence logo with biopython

Peter biopython at maubp.freeserve.co.uk
Tue Sep 18 08:51:26 UTC 2007


>> 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

Does this let you do things like:

m.weblogo("x.png", res=300)

i.e. an integer, or do you have to use a string:

m.weblogo("x.png", res="300")

One way to "fix" this (if it is a problem) would be to do this:

for k,v in kwds.items():
     values[k]=str(v)

rather than:

for k,v in kwds.items():
     values[k]=v

Anyway, given we have at least ten days until the release (Michiel will 
be away - see his email on the developers list), and this is a little 
change, I would be happy for this to go into CVS now.

Peter




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