[Bioperl-l] a basic question

[Paulo Almeida]

Hi,

Did you install BLAST? If you didn't, you should read the Description
section of this page:

http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/StandAloneBlast.html

>From that page:

"Before running StandAloneBlast it is necessary: to install BLAST on your system,
to edit set the environmental variable $BLASTDIR or your $PATH
variable to point to the BLAST directory, and to ensure that users
have execute privileges for the BLAST program."

-Paulo

On Mon, Feb 28, 2005 at 09:23:21AM -0500, yanfeng wrote:
> 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"
> 
> (I use Fedara 2.6.10)
> Fisher

-- 
Paulo Almeida
Instituto Gulbenkian de Ciencia
Apartado 14, 2781-901, Oeiras, PORTUGAL
tel  +351 21 446 46 35
fax  +351 21 440 79 70
http://www.igc.gulbenkian.pt