[Bioperl-l] no blast result

[Dave Messina]

There's a separate Bio::Tools::Run::BlastPlus module for blast+. And a
related HOWTO:
http://www.bioperl.org/wiki/HOWTO:BlastPlus



On Tue, Sep 13, 2011 at 17:09, Frank Schwach <fs5 at sanger.ac.uk> wrote:

> 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
> module.
> 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
> one.
>
> Frank
>
>
> 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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