[Biopython-dev] tiny Align.AlignInfo patch

[Michiel De Hoon]

Hi Ivan,

Thanks for the patch. But could you submit it through bugzilla? Patches
posted to mailing lists tend to get lost. (They shouldn't, but it happens a
lot in practice).

Thanks again,

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: biopython-dev-bounces at portal.open-bio.org on behalf of Ivan Rossi
Sent: Tue 12/13/2005 3:35 PM
To: biopython-dev at biopython.org
Subject: [Biopython-dev] tiny Align.AlignInfo patch
 

Dear BioPythoneers,
   I am submitting a tiny patch to the pos_specific_score_matrix method of 
Bio.Align.AlignInfo

It allows for the generation of PSSMs composed by the "alphabet+gap" symbols.

I use it all the time to generate 21-symbols PSSMs for proteins, that we use 
as inputs for neural networks and HMMs.

The patch is not invasive at all and it preserves the default behavior of 
AlignInfo.pos_specific_score_matrix()

I hope it will be considered for inclusion in the CVS.

Ivan

--
  Ivan Rossi, Ph.D. - ivan AT biodec dot com OR ivan dot rossi3 AT unibo dot
it
  BioDec s.r.l., Via Fanin 48, I-40127 Bologna (Italy)
  Phone: +39-051-4200321 - fax: +39-051-4200317 - web: www.biodec.com