[Bioperl-l] Review request: Merged hmmer2/3 parser

Kai Blin kai.blin at biotech.uni-tuebingen.de
Fri Nov 5 10:53:24 EDT 2010


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On 2010-11-05 15:17, Chris Fields wrote:

> Makes sense to me.  We're tackling some Bio::Tree revisions next
> week, my guess is we can also get this added in.  I'm really keen on
> getting 1.6.2 out sometime soon, before things get really crazy for
> me this spring.

I changed my mind about the hmmer parser just in time then, I guess. :)

> Key things to test: can specify the exact hmmer2/3 parser directly?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

That's how I started the development. But I just see I changed all tests
over, so I can't prove it. I've added some tests to show this is
equivalent. (907b7d0a2b93d4961f64)

> Can one explicitly specify the hmmer parser variant?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file
> => 'foo')

I didn't think about this, but that certainly seems reasonable. If
somebody specifies a format explicitly, we can short-circuit the other
detection code. I've added code and a couple of tests to support this.
See c9cd75df492dbef90fff.

Thanks for the input,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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