[Bioperl-l] a basic question

yanfeng yanfeng at csit.fsu.edu
Mon Feb 28 09:23:21 EST 2005

I am a beginner of Perl and Bioperl. But I need to finish a project with 
perl and bioperl.
I met a question yesterday. I googled but I still want to ask you again.

use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
$seqio_obj = Bio::SeqIO->new(-file => 'mun_lab.fasta',
                             -format => 'fasta' ); # to wrtie the 
sequence to afasta file
$seq_obj = $seqio_obj->next_seq;
#print $seq_obj->seq,"\n";
@params = (program  => 'blastn',
           database => 'db.fa' );
$blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
$report_obj = $blast_obj->blastall($seq_obj);
$result_obj = $report_obj->next_result;
print $result_obj->num_hits;
After I run it , I got the error message

-------------------- WARNING ---------------------
MSG: cannot find path to blastall
Can't call method "next_result" on an undefined value at MitoAnalyst.pl 
line 36, <GEN0> line 1.
What shall I do?
I can't fine the "blastall"

(I use Fedara 2.6.10)

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