[Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast
Rutger Vos
rvosa at sfu.ca
Sat Mar 11 21:12:12 UTC 2006
As a general rule I recommend not modifying/invoking things that start
with an underscore. I.e. don't touch _READMETHOD directly, but use
-readmethod => 'something' in the constructor, or the
$ob->readmethod('something') mutator. And I agree about the spamming.
There's a lot of people on this list who will help you if they can - but
they're all volunteers who I'm sure have their own 'urgent' matters to
attend to.
Chris Fields wrote:
>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
>
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>
--
++++++++++++++++++++++++++++++++++++++++++++++++++++
Rutger Vos, PhD. candidate
Department of Biological Sciences
Simon Fraser University
8888 University Drive
Burnaby, BC, V5A1S6
Phone: 604-291-5625
Fax: 604-291-3496
Personal site: http://www.sfu.ca/~rvosa
FAB* lab: http://www.sfu.ca/~fabstar
Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the Bioperl-l
mailing list