[Bioperl-l] Remote Blast question.

[Jason Stajich]

commited an example script in 
examples/remote_blast.pl 

If you don't have a CVS writeable account you'll probably need to wait
till after 12:30 EST to actually get the changes.

If you want to know why this is so, I've started adding to the FAQ.
http://www.bioperl.org/wiki/html/BioPerl/FAQ.html

-Jason

On Thu, 31 May 2001, Jason Stajich wrote:

> 
> Bad documentation on my part - I am preparing a script which will
> hopefully be useful and illustrate the syntax and usage of the module.
> 
> -Jason
> 
> On Thu, 31 May 2001, Ralf Sigmund wrote:
> 
> > i am also a newbie to bioperl.
> > i wrote a simple blast parser using blastcl3 output before, however i could
> > only parse for the hit Accession number and score. Now I would like to
> > extract the aligned sequences' borders.
> > i wonder if i could do better with Bio::Tools::Run::RemoteBlast.
> > 
> > i tried to understand the modules' usage by looking at the inline
> > documentation, but now i wonder how do i set @params ?
> > 
> > i tried:
> > 
> > @params = ('program' => 'blastn', 'database' => 'nr');
> > 
> > but this results in the runtime msg:
> > -------------------- WARNING ---------------------
> > MSG: trying to set program to an invalid program name (program) --
> > defaulting to blastp
> > 
> > 
> > if i use a empty @params:
> > 
> > ------------------------------------------------------------------
> > use Bio::SeqIO;
> > use Bio::Seq;
> > use Bio::Tools::Run::RemoteBlast;
> > @params = ();
> > $input = Bio::Seq->new('-id'=>"test query",
> >                          '-seq'=>"ACTAAGTGGGGG");
> > $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> > 
> > $blast_report = $factory->runblast($input);
> > -------------------------------------------------------------------
> > i allways get this error:
> > 
> > Can't locate object method "runblast" via package
> > "Bio::Tools::Run::RemoteBlast" (perhaps you forgot to load
> > "Bio::Tools::Run::RemoteBlast"?) at H:\test4.pl line 9.
> > 
> > thanks for any help ralf
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 
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> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/