[Bioperl-l] hmmer3/hmmscan parser

[Chris Fields]

On May 25, 2010, at 7:37 AM, Kai Blin wrote:

> On Tue, 2010-05-25 at 13:41 +0200, Kai Blin wrote:
> 
> Whined a little too early.
> 
>> I've tried using the hmmer3 parser for my script, but it seems like the
>> hmm_name member of the result object isn't set, and I'm using that.
>> 
>> I saw this before when trying to write a test case that integrates into
>> the Bioperl test framework.
>> (Error output is Can't locate object method "hmm_name" via package
>> "Bio::Search::Result::hmmer3Result" at t/SearchIO/hmmer3.t line 23,
>> <GEN1> line 152.)
> 
> I just found the stuff I needed to add to the hmmer3Result.pm file. I'm
> currently busy adding a comprehensive test case for this module that
> integrates into the bioperl test harness.
> 
> What's the best way to publish my additions? Do I create a fork of
> bioperl-live on Github or how is this handled?

Create a fork of the proper repository, which will eventually be bioperl-hmmer3.  However, Thomas hasn't added that code in yet; not sure how much has changed since the original deposition into bioperl-dev in March, but it's possible more has been done.  

chris

> Cheers,
> Kai
> 
> -- 
> Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
> Interfakultäres Institut für Mikrobiologie und Infektionsmedizin
> Abteilung Mikrobiologie/Biotechnologie
> Eberhard-Karls-Universität Tübingen
> Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
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>