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

Wed Jun 9 04:10:46 UTC 2010


> -----Original Message-----
> From: Peng Yu [mailto:pengyu.ut at gmail.com]
> Sent: Wednesday, 9 June 2010 4:10 p.m.
> To: Smithies, Russell
> Subject: Re: [Bioperl-l] How to run blastn with -task blastn option from
> Bio::Tools::Run::StandAloneBlastPlus?
> 
> I think it is better to document the mapping between blast options and
> bioperl options. I searched 'task', but I don't find anything. Thank
> you for letting me know.
> 
> On Tue, Jun 8, 2010 at 11:06 PM, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> > Bioperl's equivalent is blastn -task blastn -query first.fa -subject
> second.fa
> > We've just used 'method' instead of 'task'.
> >
> > You can always use the legacy_blast.pl script that comes with blast+
> then you can just use your old bl2seq commands.
> >
> > --Russell
> >
> >> -----Original Message-----
> >> From: Peng Yu [mailto:pengyu.ut at gmail.com]
> >> Sent: Wednesday, 9 June 2010 4:03 p.m.
> >> To: Smithies, Russell
> >> Subject: Re: [Bioperl-l] How to run blastn with -task blastn option
> from
> >> Bio::Tools::Run::StandAloneBlastPlus?
> >>
> >> I've solved my problem by using the wrapper. Note that this is a hack
> >> as it is not done in bioperl.
> >> $ cat `which blastn`
> >> #!/usr/bin/env bash
> >>
> >> /myinstallation/blastn -task blastn $@
> >>
> >>
> >> Anyway, I restate my original problem below.
> >>
> >> bioperl's bl2seq by default is equivalent to the following command.
> >> blastn -query first.fa -subject second.fa
> >>
> >> I want to add the option '-task blastn'.
> >> blastn -task blastn -query first.fa -subject second.fa
> >>
> >> But I don't find such option in bioperl's bl2seq.
> >>
> >> On Tue, Jun 8, 2010 at 10:58 PM, Smithies, Russell
> >> <Russell.Smithies at agresearch.co.nz> wrote:
> >> > 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
> >> >
> >>
> >>
> >>
> >> --
> >> Regards,
> >> Peng
> >
> 
> 
> 
> --
> Regards,
> Peng