[Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO
object for hmmalign?
smarkel at scitegic.com
Mon Apr 18 15:14:00 EDT 2005
Here are my proposed code changes for Bio::Tools::Run::Hmmer.
< #run hmmpfam|hmmalign|hmmsearch
> #run hmmpfam|hmmsearch
> #align one or more sequences to an existing hmm using hmmalign
> my $factory = Bio::Tools::Run::Hmmer->new('program'=>'hmmalign','hmm'=>'model.hmm');
> # Pass the factory a Bio::Seq object or a file name
> # returns a Bio::AlignIO object
> my $aio = $factory->run($seq);
> # add "-q" to make sure the banner is suppressed; note that options go
> # after hmmalign and before the file names
> my @tokens = split(/\s+/, $str);
> $str = shift(@tokens) . " -q " . join(" ", @tokens);
> open(HMM,"$str |") || $self->throw("HMMER call ($str) crashed: $?\n");
> # warning: mismatch if user has set the format using "--outformat"
> my $alignio = Bio::AlignIO->new(-fh=>\*HMM,-format=>"stockholm");
> return $alignio;
Would someone please verify that my changes are acceptable and
then do the CVS update?
Scott Markel wrote:
> 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
> hmmalign differently.
> 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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