[Bioperl-l] no blast result

Frank Schwach fs5 at sanger.ac.uk
Tue Sep 13 15:09:24 UTC 2011

Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
StandAloneBlast is still set to "blastall" - I'm not sure if it works
with blast+ too.

Manju: as I said previously, you need to check that you can run BLAST on
the command line, i.e. make sure it is actually installed on your
system. Have you done that?
You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
you can manually set the path to your BLAST executable if it is not in
your path. You have to install BLAST fisrt before you can run this
The other error you get from yuor code refers to something that is
outside of the code fragment you show here, so can't comment on that


On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> this is the perl code
>  #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO
> use Bio::Tools::Run::StandAloneBlast;
>  @params = ('database' => 'swissprot', 
>         'READMETHOD' => 'Blastn');
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
>  $blast_report = $factory->blastall($input);
>   write_blast(">rs.blast",$blast_report);
> It showing error that
> Use of uninitialized value $_[0] in join or string
> at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> MSG: cannot find path to blastall

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