[Bioperl-l] question about Bio::Tools::Run::StandAloneBlast

[Mark A. Jensen]

Hi Dimitar--
You need Bio::Tools::Run::StandAloneBlastPlus! This is in the 
most recent trunk code (not in the 1.6.1 distribution). I would 
download this from the Google mirror:
$ svn co  http://bioperl.googlecode.com/svn/bioperl-live/trunk
and
$ svn co  http://bioperl.googlecode.com/svn/bioperl-run/trunk
Both updates are necessary.
cheers 
MAJ
----- Original Message ----- 
From: "Dimitar Kenanov" <dimitark at bii.a-star.edu.sg>
To: <bioperl-l at bioperl.org>
Sent: Wednesday, April 14, 2010 6:51 AM
Subject: [Bioperl-l] question about Bio::Tools::Run::StandAloneBlast


> Hi guys,
> another question, this time about "Bio::Tools::Run::StandAloneBlast" . 
> Now i want to run 'tblastn', so i follow the guide on CAPN but it doesnt 
> matter what i do the module complains:
> 
> --------------------- WARNING ---------------------
> MSG: cannot find path to blastall
> 
> This is frustrating :) Here is my code:
> 
> ##########
> my $report_tbn="report_TBN_out.txt";
> my $dbase="/path/to/Preformatted-DB/human_genomic";
> my @params_tbn = (-program => 'tblastn',
>                                      -database => "$dbase",
>                                      -outfile => "$tmpout");
> 
> my $factory_tbn = Bio::Tools::Run::StandAloneBlast->new(@params_tbn);
> $factory_tbn->e("0.01");
> $factory_tbn->program_dir("/opt/blast/bin");_#here i tried to help it :)_
> $factory_tbn->executable('tblastn');
> 
> my $seq_stream = Bio::SeqIO->new(-file=>"$report_ss", -format => 'Fasta');
> my $seq2;
> while($seq2=$seq_stream->next_seq()){
>     my $blast_report = $factory_tbn->blastall($seq);
> }
> ##############
> 
> May be the problem is that i am using BLAST+ package where theres no 
> 'blastall' at all and 'tblastn' and all programs are standalone.
> If someone can guide me where(which module) i have to tweak a bit in 
> order to drive that programs i would be grateful :)
> Thank you for any help or directions
> 
> Cheers
> Dimitar
> 
> -- 
> Dimitar Kenanov
> Postdoctoral research fellow
> Protein Sequence Analysis Group
> Bioinformatics Institute
> A*STAR, Singapore
> email: dimitark at bii.a-star.edu.sg
> tel: +65 6478 8514
> 
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