[Bioperl-l] How to run blastn with -task blastn option from Bio::Tools::Run::StandAloneBlastPlus?
pengyu.ut at gmail.com
Tue Jun 8 22:20:39 EDT 2010
On Tue, Jun 8, 2010 at 8:28 PM, Smithies, Russell
<Russell.Smithies at agresearch.co.nz> wrote:
> Have you read the docs?
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.
>> -----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
>> I need to use Bio::Tools::Run::StandAloneBlastPlus to run the following
>> 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(
>> -query=> $seq1,
>> -subject=> $seq2
>> Thank you for you help!
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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