[Bioperl-l] Bio::Tools::Run::StandAloneBlast

[Mehta, Perdeep]

Hi,

I'm struggling to find the reason why my following test code to parse Blast output is not functioning. Just beginning to learn Bioperl and couldn't figure out what's missing.

#!/usr/bin/perl -w
#
use strict;

use Bio::Perl;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SearchIO;

  # this script will only work with an internet connection
  # on the computer it is run on

  # Get the protein sequence
   my $seq_object = get_sequence('swissprot',"ROA1_HUMAN");

  # Set database to search against
   my $DB = "/refseqdb/complete/rs_rel2";

  # Create factory for stand alone Blast and search
   my @params = ('program'  => 'blastp','database' => $DB);
   my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
   my $blast_result = $factory->blastall($seq_object);

  # Parse Blast results
   my $in = new Bio::SearchIO(-format => 'blast',
                              -file   => $blast_result);
   while( my $result = $in->next_result ) {
      while( my $hit = $result->next_hit ) {
        while( my $hsp = $hit->next_hsp ) {
          if( $hsp->length('total') > 100 ) {
            if ( $hsp->percent_identity >= 75 ) {
                print "Hit= ",        $hit->name,
                      ",Length=",     $hsp->length('total'),
                      ",Percent_id=", $hsp->percent_identity, "\n";
           }
          }
        }
      }
   }

exit;

Blastall runs fine though. Error appears to be Blast result parsing related. Here is the error message that I get;
>test.pl
Can't locate object method "algorithm" via package "Bio::SearchIO::blast" (perhaps you for
got to load "Bio::SearchIO::blast"?) at /usr/local/lib/perl5/site_perl/5.6.1/Bio/SearchIO/
Writer/TextResultWriter.pm line 146, <STREAM> line 197.

Thank you in advance for any help.
perdeep

Perdeep K. Mehta, PhD
Hartwell Center for Bioinformatics & Biotechnology
St. Jude Children's Research Hospital
Memphis, TN 38105-2794
Tel: 901-495 3774
http://www.hartwellcenter.org