[Bioperl-l] How to run blastn with -task blastn option from Bio::Tools::Run::StandAloneBlastPlus?

[Smithies, Russell]

Why are you trying to supply option '-task blastn' ??
I think the docs make it fairly clear that this is not one of the available parameters.
The option " -method => 'blastn' " (as detailed in the docs) is the one to use.
http://doc.bioperl.org/releases/bioperl-current/bioperl-run/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.html

# create a factory:
 $fac = Bio::Tools::Run::StandAloneBlastPlus->new();

# do a bl2seq
 $fac->bl2seq( -method => 'blastn',
               -query => $seq_object_1,
               -subject => $seq_object_2 );

Unless I've missed something and Bio::Tools::Run::StandAloneBlastPlus is completely broken (which is possible as it's development code) something similar to the example should work.

--Russell


> -----Original Message-----
> From: Peng Yu [mailto:pengyu.ut at gmail.com]
> Sent: Wednesday, 9 June 2010 2:21 p.m.
> To: Smithies, Russell
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] How to run blastn with -task blastn option from
> Bio::Tools::Run::StandAloneBlastPlus?
> 
> On Tue, Jun 8, 2010 at 8:28 PM, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> > Have you read the docs?
> > http://www.bioperl.org/wiki/HOWTO:BlastPlus#Running_bl2seq
> 
> Yes. But they don't say how to supply option '-task blastn' to blastn. I
> tried
> 
> my $factory = Bio::Tools::Run::StandAloneBlastPlus->new(-task='blastn');
> 
> But it doesn't work.
> 
> > Do query and subject ($seq1 and $seq2) need to be Bio::Seq objects?
> 
> I think so. I just get $seq1 and $seq2 from SeqIO. This is not my problem.
> 
> > --Russell
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Peng Yu
> >> Sent: Wednesday, 9 June 2010 1:00 p.m.
> >> To: bioperl-l at lists.open-bio.org
> >> Subject: [Bioperl-l] How to run blastn with -task blastn option from
> >> Bio::Tools::Run::StandAloneBlastPlus?
> >>
> >> Hi,
> >>
> >> I need to use Bio::Tools::Run::StandAloneBlastPlus to run the following
> >> command.
> >>
> >> blastn -task blastn -query first.fa -subject second.fa
> >>
> >>
> >> I tried the following code, which works like without the '-task
> >> blastn' option. Would you please let me know how to supply the option
> >> in Bio::Tools::Run::StandAloneBlastPlus?
> >>
> >> my $factory = Bio::Tools::Run::StandAloneBlastPlus->new();
> >>   my $result=$factory->bl2seq(
> >>     -method=>'blastn',
> >>     -query=> $seq1,
> >>     -subject=> $seq2
> >>   );
> >>   $factory->cleanup;
> >>
> >> Thank you for you help!
> >>
> >> --
> >> Regards,
> >> Peng
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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> 
> 
> --
> Regards,
> Peng