[Bioperl-l] Introducing SearchIOified HMMER v3 parser

Chris Fields cjfields at illinois.edu
Wed Mar 10 10:53:41 EST 2010

Wonderful!  Tom, thanks for your hard work!  


On Wed, 2010-03-10 at 07:30 -0800, Thomas Sharpton wrote:
> Hey everyone,
> Since HMMER version 3 went live in the middle of last month, I thought  
> it a good time to update the SearchIO parser I've been working on for  
> some time and submit the tool to the community (finally....). At the  
> moment, the module seems capable of parsing hmmsearch and hmmscan  
> outputs, both with and without the alignment option. Some aspects of  
> functionality have yet to be flushed out, but this one should be  
> capable of doing most of your day to day procedures (at least it  
> appears to on my end).
> I'd love to have people play with it and I'm happy to hear feedback,  
> criticism, development requests and bug reports.  That said, this is  
> the first code I've contributed to BioPerl, so please be gentle ;).  
> You can find the bioperl-hmmer3 package in bioperl-dev. I've included  
> a test script as well as sample hmmscan/hmmsearch report files and  
> test data in the bioperl-hmmer3 root directory.
> As an aside, BioPerl has been a wonderful resource for me and I'm glad  
> to be giving back, even if only a little. I hope this helps out at  
> least a few of you.
> All the best,
> Tom
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