[Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO
object for hmmalign?
smarkel at scitegic.com
Tue Apr 12 21:24:43 EDT 2005
It doesn't really work. It gives a SearchIO object with no
I'll take a shot at modifying Bio::Tools::Run::Hmmer to handle
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 Stajich
> jason.stajich at duke.edu
> 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 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
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
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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