[Bioperl-l] running BLAST locally

[Jason Stajich]

don't use local blast - use
Bio::Tools::Run::StandAloneBlast
for local blasts
and
Bio::Tools::Run::RemoteBlast
for remote blasts.

On Wed, 23 Jan 2002, Simon Chan wrote:

> Hi All,
>
> I'm trying to BLAST two sequences locally.  Currently, I'm reading up
> on the BLAST and LocalBlast modules.
>
> In the docs for LocalBlast, it says I need to pass a BLAST object to
> &blast_local:
>
>
>  ***Usage     : @files = blast_local($blast_object,  %namedParameters);
>               : This method is exported.
>  ***Argument  : $blast_object = object ref for a Bio::Tools::Blast.pm object.
>
>  Well, to create a BLAST object, I type this:
>
>  my %runParam = (
>                   -method   => 'local',
>                   -prog     => 'blastn',
>                   -database => 'refseq',   # I create refseq by using formatdb
>                   -seqs     => "$query",  # Bio::Seq.pm objects.
>
> );
>
> my $blast_obj = Bio::Tools::Blast->new( -run => \%runParam, -parse   => 1, -signif  => '1e-10', -strict  => 1 );
>
>
>
> But when I run it, I get the following error message:
>
> "blast_local" is not exported by the Bio::Tools::Blast::Run::Webblast module at BLAST2.pl line 76
> Can't continue after import errors at BLAST2.pl line 76
>
> But I'm not using the Webblast module!  I haven't even called it.
>
> Well, my hunch is that something is wrong with the -method => 'local' bit in the
> %runParam because the docs say that BLAST.pm
> cannot yet run local blasts.  But that's why I'm running LocalBlast.pm!
> But in order to do that, I need a defined BLAST object!
> Can everyone see the circular logic here?! ;-(
>
> If I try to "cheat" and define the blast object like so,
> my $blast_obj = Bio::Tools::Blast->new( );
>
> the error message is that I'm not passing any sequences to be blasted.
>
>
> Any help for this rookie would be much appreicated.
>
> Thanks, Everybody!
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu