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

[Smithies, Russell]

I've lost track of what your main problem is, please restate your original question?
I.e. what isn't working in Bio::Tools::Run::StandAloneBlastPlus or what part of the documentation is incorrect?


--Russell


> -----Original Message-----
> From: Peng Yu [mailto:pengyu.ut at gmail.com]
> Sent: Wednesday, 9 June 2010 3:53 p.m.
> To: Smithies, Russell
> Subject: Re: [Bioperl-l] How to run blastn with -task blastn option from
> Bio::Tools::Run::StandAloneBlastPlus?
> 
> I knew this I should use blastn as bl2seq command is not available in
> BLAST+. I'm not sure what you think I should read?
> 
> On Tue, Jun 8, 2010 at 10:47 PM, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> > I really think you need to spend more time reading and less time
> emailing.
> >
> > http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=newsncbi&part=Jan09
> > The BLAST+ package includes the ability to compare two or more sequences
> to each other in each of the search programs. Using the -subject  option
> instead of the -db will cause any of the search programs to behave as a
> BLAST 2 sequences program. This eliminates the need for the BLAST 2
> sequences utility (bl2seq) included in the traditional BLAST package.
> >
> > While it's still called 'bl2seq' in StandAloneBlastPlus, it's just a
> wrapper as there's no longer a bl2seq executable as there was with the
> older version of BLAST.
> >
> >
> > --Russell
> >
> >> -----Original Message-----
> >> From: Peng Yu [mailto:pengyu.ut at gmail.com]
> >> Sent: Wednesday, 9 June 2010 3:37 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?
> >>
> >> I made a wrapper. Then I call bl2seq in bioperl. The result changes,
> >> which means bioperl call blastn rather than bl2seq in the command
> >> line. The results are consistent between bioperl and blastn command
> >> line.
> >>
> >> $ cat `which blastn`
> >> #!/usr/bin/env bash
> >>
> >> /myinstallation/blastn -task blastn $@
> >>
> >>
> >> On Tue, Jun 8, 2010 at 10:31 PM, Smithies, Russell
> >> <Russell.Smithies at agresearch.co.nz> wrote:
> >> > 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
> >> >> >> >
> >> >>
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> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Regards,
> >> >> >> Peng
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Regards,
> >> >> Peng
> >> >
> >>
> >>
> >>
> >> --
> >> Regards,
> >> Peng
> >
> 
> 
> 
> --
> Regards,
> Peng