[Bioperl-l] local blast

Peter Schattner schattner@alum.swarthmore.edu
Mon, 06 Nov 2000 16:20:15 -0800


I canít help you with LocalBlast.pm.  However you might want to try the
new module StandAloneBlast.pm  (in the CVS main repository) which is
intended to do exactly what you are describing.  Documentation is in the
module and the scripts t/StandAloneBlast.t and
examples/standaloneblast.pl should give you examples of its usage.

Good luck!

Peter Schattner

"Bradley W. Langhorst" wrote:
> 
> 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
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