[Bioperl-l] Bio::Tools::Run::RemoteBlast return codes

Mark A. Jensen maj at fortinbras.us
Fri Jan 15 10:24:06 EST 2010


True-- blast+ allows remote dbs. I just commited a patch that makes
this easy in StandAloneBlastPlus: specify '-remote => 1' in the
factory, and downstream command calls will take care of it-
MAJ

# ex...
use Bio::Tools::Run::StandAloneBlastPlus;
use Bio::Seq;

$ENV{BLASTPLUSDIR} = $where_it_is;
my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
    -db_name => 'wgs',
    -remote => 1
    );
my $result = $fac->blastn(
    -query => 
Bio::Seq->new(-seq=>'ggcaacaaacctggtaaagaagacggcaacaagcctggtaaagaagatggcaacaagcct',
       -id=>"proteinA")
    );


1;

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Scott Markel" <smarkel at accelrys.com>
Cc: <Bioperl-l at lists.open-bio.org>
Sent: Friday, January 15, 2010 1:33 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::RemoteBlast return codes


> Scott,
>
> I think this is fine (to change the third condition and retry with a specific 
> code).  The other possibility is to simply throw different exceptions under 
> each of these circumstances, which can be caught via eval to allow a retry 
> under only certain conditions (no content, for instance).
>
> One interesting bit: I think (though I'm not sure) the new BLAST+ allows 
> remote BLAST queries from command line, similar to the legacy blastcl3.  Mark 
> just wrote up a BLAST+ wrapper, so it might be worth testing that theory out.
>
> chris
>
> PS - BTW, nice to finally meet you at GMOD!
>
> On Jan 14, 2010, at 4:58 PM, Scott Markel wrote:
>
>> We've been looking at Bio::Tools::Run::RemoteBlast after some feedback
>> from our customers.  Due to network irregularities (not sure what else
>> to call it) users see the getting of remote BLAST results as somewhat
>> random.  When results come back the hits are fine, but sometimes no
>> information comes back at all.  Retrying helps.
>>
>> In looking at RemoteBlast.pm there are four "return -1" cases.
>>
>> * $status eq 'ERROR'      (return on line 614)
>> * $line =~ /ERROR/I       (return on line 628)
>> * !$got_content           (return on line 648)
>> * !$response->is_success  (return on line 655)
>>
>> In the case of no content we'd like to retry remote BLAST.  We're happy
>> to do that part in our Pipeline Pilot Perl code wrapper for the BioPerl
>> module, but we only want to retry in that case, not the other three.
>>
>> What would happen if that third "return -1" changed to a different
>> return value?
>>
>> Scott
>>
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
>> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
>> San Diego, CA 92121                 fax:    +1 858 799 5222
>> USA                                 web:    http://www.accelrys.com
>>
>> http://www.linkedin.com/in/smarkel
>> Vice President, Board of Directors:
>>    International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>>
>>
>>
>>
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>
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