[Bioperl-l] remoteblast

Wed May 14 17:23:15 UTC 2014

Hi Scott,

That worked for me.

Thank you,

Jolyon

-----Original Message-----
From: Scott Markel [mailto:Scott.Markel at accelrys.com] 
Sent: 14 May 2014 17:18
To: Jason Stajich; Jolyon Holdstock
Cc: bioperl-l at lists.open-bio.org
Subject: RE: [Bioperl-l] remoteblast

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.
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-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jason Stajich
Sent: Wednesday, 14 May 14 2014 7:49 AM
To: Jolyon Holdstock
Cc: bioperl-l at lists.open-bio.org
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
jason.stajich at gmail.com

On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
<Jolyon.Holdstock at ogt.com>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%0ATCATAACAACCTTTTATGGTAAATAC
> TAACAGCATGCCCATTTTACATGTGAGGAAACTGAGGCTTAGATCAGGTAAGTAGCTTATTCAGTGTTGC
> TCAAGTAAATACGTTTTAAGAACCCTCAGCCTCGCTCTCCTCTTCCTCAGGGCACACTTTTTTTTTTTTC
> CTTCCTACTGTGTGAGCTGTGGTGGGAATGTTAATCGGGATGCCTGTCTTTCCCTAGTCTTGGGGTCAGG
> CAAGTGCTCAAAGTCAGGATAAGCAAACTCTCCTTCCTGGGACTCTGAGGAAAGGCTCATTGATGGGGGA
> AATGGAGGGAGTGGATTCACTCCAGCTCAGCTCCGGGACAAGATGGCCATGGAGCTCCTGCTACATAAAT
> GTCAGGGACTATCCTGGCTCCATCCTGCCTGCTTCCCTAGCTGCTGCCCAGCACTCACCTTATAAACATC
> CTTCGAGCTGGAGTTAGCCCGAATTGGTTTCTGTCCCTTGTGACCACTGAGCCCTGGCTGACACAATCAC
> AGGCTGGCGAGCAGAGGTACCAGAC&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-1
> 0&SERVICE=plain&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L
> &HITLIST_SIZE=5&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairw
> ise&PROGRAM=blastn
>
> <html>
> <head><title>An Error Occurred</title></head> <body> <h1>An Error 
> Occurred</h1>
> <p>301 Moved Permanently</p>
> </body>
> </html>
>
> ---------------------------------------------------
>
> Can anyone suggest a fix?
>
> Thanks,
>
> Jolyon
>
>
> Dr. Jolyon Holdstock,
> Oxford Gene Technology
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