[Bioperl-l] local blast

[Bradley W. Langhorst]

Okay 
so im trying to do something that should be stupid easy.

I want to blast against a small local nucleotide database.

I've modified LocalBlast.pm with the following diffs

RCS file: /home/repository/bioperl/bioperl-
live/Bio/Tools/Blast/Run/LocalBlast.pm,v
retrieving revision 1.4
diff -r1.4 LocalBlast.pm
175c175
< @Blast_dbp_local = qw( YOUR LOCAL PEPTIDE BLAST 
DATASETS HERE );
---
> @Blast_dbp_local = qw( ); #none
178c178
< @Blast_dbn_local = qw( YOUR LOCAL NUCLEOTIDE BLAST 
DATASETS HERE );
---
> @Blast_dbn_local = qw( "~bwlang/tmp/unh/blast/etr2.blast.db");
181c181
< @Blast_matrix_local  = qw( YOUR LOCAL SUBSTITUTION 
SCORING MATRICES HERE );
---
> @Blast_matrix_local  = qw( );  #na, nucleotide only
188c188
< my $program                 ='';  # your default blast program 
---
> my $program                 ='blastall';  # your default blast program 
190c190
< my $gappedAlignmentFlag     ='';  # flag to indicate if gapping is 
on or off
---
> my $gappedAlignmentFlag     ='1';  # flag to indicate if gapping is 
on or off 

but when i run like this

 %runParams = (-prog => 'blastn',
		  -method => 'local',
		  -database => "blast/etr2.blast.db",
		  -seqs => [$seqobj]);
    #blast this file against the blastdb containing all the files
    $blastObj = Bio::Tools::Blast->new( -run     => \%runParams,
                                        -parse   => 1,  
                                        -signif  => '1e-10',
                                        -strict  => 1,
				      );
I get

"blast_local" is not exported by the 
Bio::Tools::Blast::Run::Webblast module at 
./find_common_elements.pl line 49

so I go over there and make these changes

diff -r1.17 Blast.pm
1281,1282c1281,1282
<     require Bio::Tools::Blast::Run::Webblast; 
<     Bio::Tools::Blast::Run::Webblast->import(qw(&blast_local));
---
>     require Bio::Tools::Blast::Run::LocalBlast; 
>     Bio::Tools::Blast::Run::LocalBlast->import(qw(&blast_local));
But this fails very badly with inability to resolve _rearrange...

Is this local blasting stuff supposed to be working?
Did I make some error in calling the blast?
Or in the customizatoin of that LocalBlast.pm module?

thanks!

brad