[Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO object for hmmalign?

[Scott Markel]

Jason,

It doesn't really work.  It gives a SearchIO object with no
hits.

I'll take a shot at modifying Bio::Tools::Run::Hmmer to handle
hmmalign differently.

Scott

Jason Stajich wrote:

> That is curious.  Is it even a proper searchIO object - I can't imagine 
> it would work? I assume you know what it would take in Tools::Run::HMMER 
> to do something different for hmmalign runs.
> 
> -jason
> -- 
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> On Apr 12, 2005, at 8:23 PM, Scott Markel wrote:
> 
>> I'm curious as to why Bio::Tools::Run::Hmmer returns a
>> SearchIO object when the program is hmmalign.  I would
>> have expected an AlignIO object since the result of an
>> hmmalign execution is a Stockholm formatted alignment file.
>>
>> I expect that I'm missing something obvious, but I don't
>> see it.  An online search, including the mailing list
>> archive, didn't help.
>>
>> Scott
>>
>> -- 
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect  email:  smarkel at scitegic.com
>> SciTegic Inc.                       mobile: +1 858 205 3653
>> 9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
>> San Diego, CA 92123                 fax:    +1 858 279 8804
>> USA                                 web:    http://www.scitegic.com
>>
>>
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> 
> 

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com