[Bioperl-l] cannot find path to blastall

[hafiz yusof]

i have done running this code, and i getting this
error;

-------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------
Can't call method "next_result" on an undefined value
at blast1.pl line 22, <GEN0> line 1.
BEGIN failed--compilation aborted at blast1.pl line
29.




#!/usr/bin/perl

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


BEGIN
{

$ENV{PATH}=":/home/bioinfo/Laurent/Utils/Blast/blast-2.2.10/bin/:";


my $Seq_in = Bio::SeqIO->new (-file
=>"/home/hafiz/bioperl/fasta", -format => 'fasta');
my $query = $Seq_in->next_seq();

my $factory =
Bio::Tools::Run::StandAloneBlast->new('program'  =>
'blastp',
                                                 
'database' => 'ecoli.nt',
                                                 
_READMETHOD => "Blast"
                                                  );
my $blast_report = $factory->blastall($query);
my $result = $blast_report->next_result;

while( my $hit = $result->next_hit()) {
    print "\thit name: ", $hit->name(), "
significance: ",

$hit->significance(), "\n";}

}














--- Laurent DOUCHY <l.douchy at gmail.com> wrote:

> try with this on the top of your code.
> 
> #!/usr/bin/perl
>  
> use strict;
> use Bio::SeqIO;
> use Bio::Tools::Run::StandAloneBlast;
> 
> BEGIN 
> {
> 
>
$ENV{PATH}=":/home/bioinfo/Laurent/Utils/Blast/blast-2.2.10/bin/:";
> }
> 
> ...
> 
> 2005/6/22, hafiz yusof <khufaz83 at yahoo.com>:
> > I'm trying to set up a standalone blast and I'm
> > getting an error message;
> > 
> > MSG: cannot find path to blastall
> > 
> > and i have running this code under Linux and i
> also
> > haven't find blastall file in /usr/local/bin/,
> what
> > should i do?
> > 
> > code:
> > 
> > #!/usr/bin/perl
> > 
> > use strict;
> > use Bio::SeqIO;
> > use Bio::Tools::Run::StandAloneBlast;
> > 
> > my $Seq_in = Bio::SeqIO->new (-file
> > =>"/home/hafiz/bioperl/fasta", -format =>
> 'fasta');
> > my $query = $Seq_in->next_seq();
> > 
> > my $factory =
> > Bio::Tools::Run::StandAloneBlast->new('program' 
> =>
> > 'blastp',
> > 
> > 'database' => 'ecoli.nt',
> > 
> > _READMETHOD => "Blast"
> >                                                  
> );
> > my $blast_report = $factory->blastall($query);
> > my $result = $blast_report->next_result;
> > 
> > while( my $hit = $result->next_hit()) {
> >     print "\thit name: ", $hit->name(), "
> > significance: ",
> > 
> > $hit->significance(), "\n";}
> > 
> > Send instant messages to your online friends
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> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> >
>
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> >
> 


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