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

[Jason Stajich]

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.
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