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

[Peng Yu]

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