[Bioperl-l] can't locate object method "next_result" (probably a simple problem)

Andrew Norman anorman at stanford.edu
Thu Mar 16 18:53:42 EST 2006


Hi Everyone

I'm brand new to bioperl and object oriented programming in general.  I've been trying some of the example scripts in the HOWTO and I ran into the following error (I'm using bioperl v. 1.2.3, windows XP) while trying to get some blast results to print:

"can't locate object method "next_result" via package "Bio::Seq" at blast_tetra.pl"

Here's the script:

use Bio::Seq;
use Bio::SeqIO;
use Bio::Tools::Run::StandAloneBlast;



open OUTPUT, ">>blast_output.txt";

my $file_obj = Bio::SeqIO->new(-file => "blast_input.fasta", -format => "fasta" );
my @params = (program  => 'blastx', database => 'Tetraodon_nigroviridis.TETRAODON7.mar.pep.fa', _READMETHOD => 'SearchIO' );
my $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);


while (my $seq_obj = $file_obj->next_seq){   
    
 my $report_obj = $blast_obj->btblastall($seq_obj);
 
 my $result_obj = $report_obj->next_result;
  print OUTPUT $result_obj->num_hits,"\t",$result_obj->hits, "\n";



}

close OUTPUT;


I'd appreciate any help anyone has to offer.  Thanks!

andy


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