[Biopython-dev] Refactoring motif analysis code

[Bartek Wilczynski]

On Mon, Dec 1, 2008 at 10:07 PM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:

> Thanks for all these changes.
> I remember that I wrote a mail to TAMO's authors when I was using it.
> They seemed to be interested in integrating the code with biopython,
> so maybe the license issue could be superated.
> It's up to you, whether you want to reimplement all the functions they
> have or not.

I have to say I haven't done anything yet towards integrating TAMO
with biopython.
So far, my own code was doing the job for me, and since there was a
certain learning curve to get into TAMO,
I didn't look closely into it. I've looked more carefully now at it
and I have two general thoughts:
- There is a number of features in TAMO, for which there is no
counterpart in Bio.Motif. Just by looking at module names I've found:
 - MDscan parser
 - their own EM motif finding scheme (some kind of EM method)
 - several motif comparison functions from MotifCompare
 - a lot of nice little methods for motifs like textLogo, giflogo, etc.
- There is quite an overlap between biopython and TAMO. They
implemented their own Sequence handling, FASTA Parser, clustering
module etc.  There will be some gruntwork with integrating their code
into Biopython (findining and reconciling the overlaps)

I also have to say, that I'm a bit scared by copright statements in
the TAMO code, saying it belongs to the Whitehead institute. I don't
want to be overly pessimistic, but the process of releasing this code
under biopython license might be slow.

What I think is the best way to go is to clean up current mess with
Bio.Alignace and Bio.MEME, and then ask people for contributions.
If TAMO developers would be willing to contribute I'll be happy to
help with integration into biopython. It will take some time anyway,
so I wouldn't delay the inclusion of Bio.Motif into Biopython.

cheers
Bartek



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