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

[Smithies, Russell]

Without digging thru the code, I think the developer can call the parameters whatever he likes and if he wants to use "-method " instead of "-task " there's probably a good reason (right MAJ?)

If you write code as in the docs, does it give you the same results as when you run bl2seq manually from the command line?
When you run it via BioPerl, does " -method => 'blastn' " give you a different result to " -method => 'megablast' " or " -method => 'dc-megablast' "



--Russell



> -----Original Message-----
> From: Peng Yu [mailto:pengyu.ut at gmail.com]
> Sent: Wednesday, 9 June 2010 3:12 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?
> 
> See the help page of blastn. By default blastn use the option "-task
> megablast", which is less sensitive than the option "-task blastn".
> 
> $ blastn -help
> ....
>  -task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
>                   'megablast' 'vecscreen' >
>      Task to execute
>      Default = `megablast'
> ...
> 
> On Tue, Jun 8, 2010 at 10:09 PM, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> > 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
> >> >
> =======================================================================
> >> > Attention: The information contained in this message and/or
> attachments
> >> > from AgResearch Limited is intended only for the persons or entities
> >> > to which it is addressed and may contain confidential and/or
> privileged
> >> > material. Any review, retransmission, dissemination or other use of,
> or
> >> > taking of any action in reliance upon, this information by persons or
> >> > entities other than the intended recipients is prohibited by
> AgResearch
> >> > Limited. If you have received this message in error, please notify
> the
> >> > sender immediately.
> >> >
> =======================================================================
> >> >
> >>
> >>
> >>
> >> --
> >> Regards,
> >> Peng
> >
> 
> 
> 
> --
> Regards,
> Peng