[Bioperl-l] supporting hmmer3 in bioperl-run and bioperl-live

Chris Fields cjfields at illinois.edu
Wed Feb 11 14:05:46 UTC 2009

On Feb 11, 2009, at 7:48 AM, Dave Messina wrote:

> HMMER3 is still in early alpha IIRC, but I did get an Infernal  
> parser working pre-1.0 release so...
> I am somewhat interested in doing this, but I'm a little reluctant  
> to do so yet because formats and options are a moving target.
> HMMer's author Sean Eddy wrote on his blog:
> The core of H3's functionality seems stable to me, but all the stuff  
> that you see — the applications, the command line options, the i/o  
> formats — is deliberately still protoypical and fluid.
> So personally I'm inclined to wait, but don't let that stop anyone  
> else from jumping ahead.
> D

If someone pursues this, I suggest keeping a separate HMMER3 set of  
modules.  Either use something like Bio::SearchIO::hmmer3,  
Bio::Tools::Run::Hmmer3, or separate out the HMMER2 code from HMMER3  
(wrap them in their own distinct 'plugin' and load them on the fly  
within Bio::SearchIO::hmmer/Bio::Tools:Run::Hmmer).

There will likely be significant enough differences between output (as  
indicated by Sean Eddy's blog) and program parameters/options, it  
keeps the HMMER2 code fast (no additional regex/parameter checks for  
HMMER3-specific output), and it makes deprecating the HMMER2 code  
easier a few years or so down the road.


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