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

[Peng Yu]

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