[Bioperl-l] Remote Blast question.

[Jason Stajich]

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