[Bioperl-l] cannot find path to wublast

Jyoti Shah jyotikshah at gmail.com
Wed Mar 22 16:24:35 EST 2006


Hi,

I had a question regadring the usage of standaloneblast to parse wublast
results. I am comparatively new with bioperl and any help would be greatly
appreciated :-)

I have previously used standaloneblast to parse NCBI blast results and it
seems to work fine but when I tried the similar approach with the wublast ,
I got the following error message:

-------------------- WARNING ---------------------
MSG: cannot find path to wublast
---------------------------------------------------
Can't call method "next_result" on an undefined value at ./wu-blast.pl line
20.

The script I have used for this is as follows:

#!/usr/bin/perl
use lib "/home/admin/bioperl-1.4/";
$db='/unigene/human/Hs.seq.uniq';

use Bio::Tools::Run::StandAloneBlast;
BEGIN { $ENV{PATH} = '/home/wustl/wu-blast'; }
BEGIN { $ENV{BLASTDATADIR} = '/home/databases/'; }
use Bio::Seq;
use Bio::LocatableSeq;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::SearchIO;
@params = ('program' => 'wublastn',
                  'database' => $db);
$seqn = "AAGGCCGTGACCC";
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
$input = Bio::Seq->new(-id  =>"test_query",
                                  -seqn=> $seqn);
my $blast_report = $factory->wublast($input);
my $result = $blast_report->next_result;
while(my $hit = $result->next_hit())
       {
       $name=$hit->name();
       $desc=$hit->description();
       print "Name $name\tDesc $desc\n";
       }



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