[Bioperl-l] Introducing SearchIOified HMMER v3 parser
thomas.sharpton at gmail.com
Wed Mar 10 10:30:37 EST 2010
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,
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