[Bioperl-l] a basic question

[Sean Davis]

----- Original Message ----- 
From: "yanfeng" <yanfeng at csit.fsu.edu>
To: <bioperl-l at bioperl.org>
Sent: Monday, February 28, 2005 9:23 AM
Subject: [Bioperl-l] a basic question


> Hi,
> 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"

Did you install blast from NCBI (go to www.ncbi.nih.gov and find the blast 
site, download it, and install it according to their instructions)?  In 
order to run standalone blast, you will need to install blast.

Sean