[Bioperl-l] supporting hmmer3 in bioperl-run and bioperl-live
cjfields at illinois.edu
Wed Feb 11 09:05:46 EST 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.
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
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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