[Bioperl-l] cannot find path to blastall

[Brian Osborne]

James,

Does:

my @params = (program => 'blastp',
              database => '"/home/j1gregor/transposon/subtilis');

work?

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of James Gregory
Sent: Tuesday, March 15, 2005 4:30 PM
To: Brian Osborne
Cc: bioperl-l at bioperl.org
Subject: RE: [Bioperl-l] cannot find path to blastall


fixed it, i thought you could manually set the path within the perl
script.  I just added blastall to usr/bin/local (on a unix machine) and it
works, except now I'm having other troubles.

i ran
formatdb -i SLR16.1_prot.txt -o T -n subtilis

where SLR16.1_prot.txt is a fasta formatted file.  I get these files from
formatdb.

subtilis.phr  subtilis.pin  subtilis.psd  subtilis.psi  subtilis.psq

from my understanding the .psq file is the one you want so i have

#create seq object for blast
my $blast_seq = Bio::Seq->new( '-id' => "$seq_name",
                                '-seq' => "$prot_seq");


#set BLAST params
my @params = (program => 'blastp',
               database => '/path/to/file/subtilis.psq');
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);


#BLAST
my $blast_report = $factory->blastall($blast_seq);


but i'm getting this error:

Could not find index files for database
/home/j1gregor/transposon/subtilis.psq

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: blastall call crashed: 256 /usr/local/bin/blastall -p  blastp  -d
"/home/j1gregor/transposon/subtilis.psq"  -i  /tmp/onOzNhelp8  -o
/tmp/HlsmLpIFrT

STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.3/Bio/Root/Root.pm:328
STACK: Bio::Tools::Run::StandAloneBlast::_runblast
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:732
STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:680
STACK: Bio::Tools::Run::StandAloneBlast::blastall
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:536
STACK: GFP_find.pl:85

thanks again,
James

On Tue, 15 Mar 2005, Brian Osborne wrote:

> James,
>
> On Unix? Windows? Cygwin? Something else? Also is "/path/to/blastall" the
> actual location of blastall? On a Linux machine this might be something
like
> "/usr/local/bin/blastall". We need to know a bit more.
>
> Brian O.
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of James Gregory
> Sent: Tuesday, March 15, 2005 4:08 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] cannot find path to blastall
>
>
>
> I'm trying to set up a standalone blast and I'm getting an error message
> that says
>
> MSG: cannot find path to blastall
>
> code:
>
> my @params = (program => 'blastp',
>               database => 'db.psq');
> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $path = '/path/to/blastall/';
> $path = $factory->program_path($path);
>
> #BLAST
> my $blast_report = $factory->blastall($blast_seq);
>
> any help would be appreciated.
>
> James Gregory
> University of California, San Diego
> Department of Biological Sciences
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
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