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

[Peng Yu]

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