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

Peng Yu pengyu.ut at gmail.com
Wed Jun 9 14:51:31 UTC 2010 

My original code use -method=>'blastn' as
Bio::Tools::Run::StandAloneBlastPlus's option, which is not equivalent
to blast+'s command line option -task blastn.


On Tue, Jun 8, 2010 at 11:10 PM, Smithies, Russell
<Russell.Smithies at agresearch.co.nz> wrote:
>
>
>> -----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
>> >> >> >> >> >> >
>> >> >> >> >>
>> >> >>
>> =======================================================================
>> >> >> >> >> >> > 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
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Regards,
>> >> >> >> Peng
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Regards,
>> >> >> Peng
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Regards,
>> >> Peng
>> >
>>
>>
>>
>> --
>> Regards,
>> Peng
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Regards,
Peng

More information about the Bioperl-l mailing list