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Gmane
From: Scott Markel <Scott.Markel <at> accelrys.com>
Subject: Re: remoteblast
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 14th May 2014 16:18:26 UTC (over 2 years ago)
In this case the code change is straightforward and doesn't require any
change to Bio::Tools::Run::RemoteBlast.  The constructor can take a
URL_BASE argument, so just pass in the new URL (http://blast.ncbi.nlm.nih.gov/Blast.cgi).
 This will overwrite the old URL (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi)
hard-coded in Bio::Tools::Run::RemoteBlast.  We made this change to the
remote BLAST components in the Pipeline Pilot Sequence Analysis collection
and things have been fine.

    my @parameters = ("-prog"       => $program,
                      "-data"       => $database,
                      "-readmethod" => 'xml',
                      "-URL_BASE"   => $url);
    
    my $blastFactory = Bio::Tools::Run::RemoteBlast->new(@parameters);

Hope this helps.

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  [email protected]
Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
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-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Jason Stajich
Sent: Wednesday, 14 May 14 2014 7:49 AM
To: Jolyon Holdstock
Cc: [email protected]
Subject: Re: [Bioperl-l] remoteblast

So the BLAST services changed - not sure if we will still even support perl
based - it will require a developer tracking and testing to the new NCBI
resources since the have discontinued the older submission CGI resource.

You can run remote blast with commandline tool from NCBI as an alternative.

I think we will need to have a developer volunteer who wants to keep
working on tracking the webservices for NCBI to keep this module working.

Jason

Jason Stajich
[email protected]


On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
<[email protected]>wrote:

> Hi,
>
> I have a script that runs blast jobs against the databases at the NCBI.
>
> I use the  Bio::Tools::Run::RemoteBlast module for the blasting.
>
> It was working but is not now.
>
> The following is an example of the response I now get:
>
> --------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.006901
> Content-Length: 788
> Content-Type: application/x-www-form-urlencoded
>
>
>
DATABASE=nr&QUERY=%3EHCV-54_contig_15+%0D%0ATCATAACAACCTTTTATGGTAAATACTAACAGCATGCCCATTTTACATGTGAGGAAACTGAGGCTTAGATCAGGTAAGTAGCTTATTCAGTGTTGCTCAAGTAAATACGTTTTAAGAACCCTCAGCCTCGCTCTCCTCTTCCTCAGGGCACACTTTTTTTTTTTTCCTTCCTACTGTGTGAGCTGTGGTGGGAATGTTAATCGGGATGCCTGTCTTTCCCTAGTCTTGGGGTCAGGCAAGTGCTCAAAGTCAGGATAAGCAAACTCTCCTTCCTGGGACTCTGAGGAAAGGCTCATTGATGGGGGAAATGGAGGGAGTGGATTCACTCCAGCTCAGCTCCGGGACAAGATGGCCATGGAGCTCCTGCTACATAAATGTCAGGGACTATCCTGGCTCCATCCTGCCTGCTTCCCTAGCTGCTGCCCAGCACTCACCTTATAAACATCCTTCGAGCTGGAGTTAGCCCGAATTGGTTTCTGTCCCTTGTGACCACTGAGCCCTGGCTGACACAATCACAGGCTGGCGAGCAGAGGTACCAGAC&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=plain&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&HITLIST_SIZE=5&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastn
>
> 
> An Error Occurred
> 
> 

An Error Occurred

>

301 Moved Permanently

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CD: 3ms