[Biopython-dev] Support for standalone version of AlignACE motif search program

Jeffrey Chang jefftc at stanford.edu
Wed Jul 23 16:40:00 EDT 2003

Hey Bartek,

Your package looks very nice.  I'd be happy to check it in under 
Bio.AlignAce.  I am getting ready to put out a release, so it will have 
to be done after that goes out.

Please take a look at the documentation for contributing code to 
Biopython the website at:

In particular, please read the "Submitting Code" section and make sure 
you agree with it.  Mostly, it is just to make sure that you want to 
support your code, and that you agree to the Biopython license.  Let me 
know if everything seems good to you.


On Wednesday, July 23, 2003, at 11:53  AM, Bartek Wilczynski wrote:

> Hello All,
> I have written a wrapper for standalone version of AlignACE software.
> (http://atlas.med.harvard.edu/) It's still far from perfect, but it 
> serves well
> for me.
> It includes the Application class, AlignAceStandalone.AlignAce() 
> function to run
> it, Scanner and Parser. As a result of the code like this:
> from Bio.AlignAce.AlignAceStandalone import AlignAce
> from Bio.AlignAce.Parser import AlignAceParser
> result = AlignAce("test.seq")
> motifs = AlignAceParser().parse(result[1])
> you have set of motifs found by AlignAce in the sequences from the 
> FASTA file
> test.seq.
> It assumes that the AlignACE executable is in your path, and the 
> test.seq file
> is in current directory.
> This module includes also the implementation of a motif object. I'm 
> not sure if
> my implementation is general enough to become a BioPython structure, 
> but I think
> there's a need for something like that. Probably it should be called
> Bio.SeqMotif and include different things (more than my simplistic 
> idea).
> I would be really glad if You will find it interesting enough to 
> include it to
> the biopython cvs, any comments/remarks are more than welcome.
> -- 
> regards
>    Bartek Wilczyñski
> <AlignAce.tar.gz>_______________________________________________
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