[Bioperl-l] problems with: Bio::Tools::Run::RemoteBlast

Sendu Bala bix at sendu.me.uk
Tue Oct 17 11:14:07 EDT 2006


Bertrand Beckert wrote:
> hi,
> 
> I am running a large number of blasts via a connexion to ncbi blast
> page ('http://www.ncbi.nlm.nih.gov/blast/Blast.cgi').
> I try to use 'Bio::Tools::Run::RemoteBlast' but unfortunately I have
> some problems.
[snip]
> In the documentation it wrote that $result=$factory->retrieve_blast
> ($rid) return when it work a Bio::Tools::Bplite or Bio::Tools::Blast
> object. In my case it returns a Bio::SearchIO::blast... I don't
> understand why I don't have the good type of object return (see PART I).

I take it you're using some old version of Bioperl where unfortunately 
the documentation was incorrect. In fact you're supposed to get a 
Bio::SearchIO object, so it is a good thing that you are. The latest 
version of Bioperl has (as far as I can see) correct documentation and 
behaviour.

Bio::Tools::Bplite and Bio::Tools::Blast are deprecated. You want 
Bio::SearchIO::blast. All is well.


> I also try to resolve the problem by replace the foreach loop in my
> script by a new one in order to explore the blast page result but it
> also don't work (see part II).

I'm not really sure what problem you might be facing there, but take a 
look at some up-to-date documentation, using the new example code:

http://doc.bioperl.org/bioperl-live/Bio/Tools/Run/RemoteBlast.html


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