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

[Bartek Wilczynski]

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




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