[Bioperl-l] StandAloneBlastPlus

Waldenmaier, Hans Eugene waldenhe at muohio.edu
Fri Sep 24 15:15:48 EDT 2010

Hello Bioperl Masters,

I am trying to perform a local blast with a query list of fasta files against a db of other fasta files.  I am attempting to use the Bio::Tools::Run::StandAloneBlastPlus module.  I have downleaded from the NCBI website BLAST+ 2.2.24+ and installed on my ubuntu machine.  I am using bioperl-1.5.2.

so the snibbit of code that is giving me errors is below:

my $seq_obj = Bio::Seq->new(-id =>$accn, -seq =>$seq);
my $report_obj = $blast_obj->blastall($seq_obj);
my $result_obj = $report_obj->next_result;
print $result_obj->num_hits;

The error I am getting is:

--------------------- WARNING ---------------------
MSG: cannot find path to blastall
Can't call method "next_result" on an undefined value at /media/C8B3-4A4A/Bioinformatics 1.1 beta/BioPerl/bioperl.pm line 284.

I think the real problem is the "cannot find path to Blastall.

>From reading around on different forums I have to make  a  .ncbirc text file with the location of BLAST+2.2.24+ on my machine.  I have that file in my /home folder.

How do I get  StandAloneBlastPlus synced up with BLAST+2.2.24+ ?  Am I approaching this right?


Hans Waldenmaier

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