[Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast

[Chris Fields]

What version of bioperl are you using?  What OS?  Always a good idea  
to give these details.  Although I believe there is a major reworking  
of the Bio::Tools::Run BLAST modules planned I'm pretty sure that  
everything still works, at least in the latest developer version.   
Lots of people are running it so I'm guessing something is wrong with  
the logic here otherwise we would have heard about this a while ago.

I'm not an expert about this module either but I believe Brian's  
right about _READMETHOD.   When using SearchIO directly this is set  
using "-readmethod => 'SearchIO'" for text, 'blastxml' for xml, and  
'blasttable' for tabular.  According to the POD for StandAloneBlast  
SearchIO::blast is default;  have you tried not using that flag  
(removing it)?  Does the matrix you're using exist in the /data  
directory?

Chris

On Mar 11, 2006, at 12:47 AM, neeti somaiya wrote:

> Hi,
> I am running standalone blast and I wanna use a particular e value,  
> gap open
> and extension cost and matrix.
> I have tried using all possible ways:
>
> 1)
> @params = ('program'  => 'blastn','database' => 'human.rna.fna',  
> _READMETHOD
> => "Blast",'e' => '0.0001', 'Matrix' => 'BLOSUM80' );
> my $factory = new Bio::Tools::Run::StandAloneBlast(@params);
>
> 2)
> @params = ('program'  => 'blastn','database' => 'human.rna.fna',  
> _READMETHOD
> => "Blast",'e' => '0.0001', 'M' => 'BLOSUM80' );
> my $factory = new Bio::Tools::Run::StandAloneBlast(@params);
>
> 3)
> my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>  
> 'blastn',
>                                                  'database' => '
> human.rna.fna',
>                                                  _READMETHOD =>  
> "Blast"
>                                                  );
> $factory->e(0.0001);
> $factory->G(-11);
> $factory->E(-1);
> $factory->M('BLOSUM80');
>
> 4)
> my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>  
> 'blastn',
>                                                  'database' => '
> human.rna.fna',
>                                                  _READMETHOD =>  
> "Blast"
>                                                  );
> $factory->e(0.0001);
> $factory->MATRIX('BLOSUM80');
> $factory->GAP(-11);
> $factory->EXTENSION(-1);
>
> But, still, the blast results show just the e value change, but no  
> changes
> from default in the matrix used or gap opening and extension  
> penalities.
>
> What should I do?
>
> Please help.
>
>
> On 2/23/06, Chris Fields <cjfields at uiuc.edu> wrote:
>>
>> Have you tried this to see if it works?  The blast report itself  
>> should
>> tell
>> you if everything is set correctly.  Use 'perldoc
>> Bio::Tools::Run::StandAlone::Blast', which explains everything.  I  
>> don't
>> know if the example script works but the test script  
>> StandAloneBlast.t (in
>> /t) should; that will give you plenty of examples for setting  
>> parameters.
>>
>> And please, don't spam the bioperl-l list with repeated emails  
>> (four at
>> last
>> count over 2 1/2 hours).
>>
>> Christopher Fields
>> Postdoctoral Researcher - Switzer Lab
>> Dept. of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of neeti somaiya
>>> Sent: Thursday, February 23, 2006 4:13 AM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] urgent help required - syntax for using
>>> paramatersdifferent from default in standalone blast
>>>
>>> Hi,
>>>
>>> I am running standalone blast and I wanna use a particular e  
>>> value, gap
>>> open
>>> and extension cost and matrix. Is the following the correct  
>>> syntax for
>> the
>>> same :
>>>
>>>                                 my $Seq_in = Bio::SeqIO->new (- 
>>> file =>
>>> $file, -format => 'fasta');
>>>                                 my $query = $Seq_in->next_seq();
>>>                                 my $factory =
>>> Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastn',
>>>                                                  'database' => '
>>> human.rna.fna',
>>>                                                  _READMETHOD =>  
>>> "Blast"
>>>                                                  );
>>>                                 $factory->e(0.0001);
>>>                                 $factory->G(-11);
>>>                                 $factory->E(-1);
>>>                                 $factory->M('BLOSUM80');
>>>
>>>                                 my $blast_report =
>>> $factory->blastall($query);
>>>                                 my $result = $blast_report- 
>>> >next_result;
>>>
>>> --
>>> -Neeti
>>> Even my blood says, B positive
>>>
>>> --
>>> -Neeti
>>> Even my blood says, B positive
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
>
> --
> -Neeti
> Even my blood says, B positive
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign