[Biopython-dev] Refactoring motif analysis code

[Bartek Wilczynski]

Hello All,

Currently, there are two packages dealing with motif analysis in biopython :
Bio.AlignAce (written by me) and Bio.MEME (written by Jason Hackney).

Both of them are quite old and they were developed independently so
the functionality is largely overlapping.
Particularly the files AlignAce/Motif.py  and MEME/Motif.py contain
almost identical functionality useful for
anyone interested in motif analysis of  writing a parser for yet
another motif searching tool.

I'd like to change this and create a new library called Bio.Motif,
which would contain:
-Motif class for all general functionality concerning motif objects:
i/o, comparisons, sequence scanning
-AlignAce Parser
-MEME Parser

When this is completed, we could deprecate the AlignAce and MEME
modules. For AlignAce I have most of the code
already written, I need to rewrite portions of MEME parser to work
with different motif implementation (not a major pain).
Then I just need to polish it a bit and provide tests and a short tutorial.

After this rather long intro I'd like to ask about several things:
- Are there many Bio.AlignAce or Bio.MEME users who would be unhappy
about deprecating them?
- Are there any features which people would find valuable in Bio.Motif
- Both MEME and AlignAce are DNA-oriented, I've never worked on
Protein motifs myself, but I'd like to know whether anyone is
interested in using Bio.Motif for that

Any comments/ideas are welcome

cheers
Bartek

-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433