[Bioperl-l] cannot find path to blastall

[Laurent DOUCHY]

hum ... sory but you must replace the path to blast program. I think
that the database path is important to.

#!/usr/bin/perl

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


BEGIN
{
$ENV{PATH}=":yourPath/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' => 'yourPath/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";}



2005/6/22, hafiz yusof <khufaz83 at yahoo.com>:
> 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";}
> > >
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