[Bioperl-l] hmmer3/hmmscan parser

Kai Blin kai.blin at biotech.uni-tuebingen.de
Tue May 25 11:41:59 UTC 2010

On Mon, 2010-05-24 at 17:46 -0700, Thomas Sharpton wrote:

Hi Tom,

> To clarify, I have constructed a SearchIO parser for hmmer3 hmmscan and
> hmmsearch output. It appears to be fully functional and I have had a handful
> of users test and integrate this module.

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'm happy to work on this a bit myself if you're not working on this
anyway, so we don't duplicate efforts. I just don't get why the hmm_name
isn't picked up correctly, and I haven't been able to figure out how to
get at the output that $self->debug() when running the tests. Oh well,
it's a learning experience in any case.


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
D-72076 Tübingen                        Fax : ++49 7071 29-5979
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben

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