[Bioperl-l] hmmer3/hmmscan parser

[Kai Blin]

On Tue, 2010-05-25 at 11:33 -0700, Thomas Sharpton wrote:

Hi Thomas,

> http://github.com/bioperl/bioperl-hmmer3
> 
> Please use this updated code before making any significant changes - I  
> think I may have already fixed the bug you brought up earlier (but  
> maybe not?). Do let me know if you have any problems getting ahold of  
> this data or if you find any bugs in the code I'd deposited.  Still  
> getting my head wrapped around github.

I've seen the repo, and forked from it already to push my changes. Some
of the folks from IRC gave me write access and Chris Fields actually
pushed my changes.

Most notable about the changes is probably a bit hidden by the noise,
but I've changed the Hit->raw_score to contain the overall score, not
the "best domain" score.

> Trying to integrate hmmer3 into the old hmmer searchIO module was the  
> original idea. But after talking to some of the BioPerl gurus and  
> considering the inherent differences between hmmer3 and hmmer2 (at  
> least during beta, though there are still some major output report  
> differences in the live release), we decided as separate module would  
> be ideal.

Some of the folks on IRC suggested that we might want to integrate the
hmmer.pm parser as well, modularizing this a bit and loading the correct
parser depending on the requested format.

> This is an obvious statement, but I feel it's important to be clear on  
> these matters - you should feel free to make any and all contributions  
> to the development of this module as you see fit.  BioPerl has been  
> wonderful to me and I started this module to give a little back, but  
> this remains community generated software.

I'm planning on adding even more tests, but the basic features for
hmmscan parsing seem to be there. I'm currently running an extensive
test run on real genome data, hopefully I can see the results of that in
a couple of days.

Cheers, and thanks for the help,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Interfakultäres Institut für Mikrobiologie und Infektionsmedizin
Abteilung Mikrobiologie/Biotechnologie
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Deutschland
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben