[Bioperl-l] RemoteBlast and psiblast

Wed, 11 Sep 2002 08:08:28 -0400 (EDT)

Clearly this a problem of going through your proxy.

I don't think the -proxy works as an init parameter (but it should be
added, patched welcomed).

You should be able to do
$factory->proxy('XXX', 'http');
before you call the submit_report and it should work.

Someone should make the -proxy parameter available in most of the modules
which do connect through HTTP or FTP which would then pass through to the
$obj->proxy method.

-jason
On Wed, 11 Sep 2002, Hadas Leonov wrote:

> Hi,
> I have encountered the following error message while running a simple
> remote blast script:
>
> -------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: libwww-perl/5.64
> Content-Length: 541
> Content-Type: application/x-www-form-urlencoded
>
> PROGRAM=blastp&QUERY=MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD&DATABASE=nr&SERVICE=plain&CMD=Put&EXPECT=1e-3&CDD_SEARCH=off&FORMAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L
>
> <HTML>
> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> <BODY>
> <H1>An Error Occurred</H1>
> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Timeout)
> </BODY>
> </HTML>
>
> ---------------------------------------------------
>
> while using the following script:
>
> ---
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> use Bio::Tools::Run::RemoteBlast;
>
> my $Seq_in = Bio::SeqIO->new (-file => $ARGV[0], -format => 'fasta');
> my $query = $Seq_in->next_seq();
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(
>         '-prog'  => 'blastp',
>         '-data' => 'nr',
>         '-proxy' => 'http://wwwproxy.huji.ac.il:8080',
>         _READMETHOD => "Blast"
>         );
>
> my $blast_report = $factory->submit_blast($query);
> ---
>
> I don't think the problem is my proxy, because I can connect to the same
> site (www.ncbi.nlm.nih.gov) through wget.
>
> any idea what's going on? I'm using bioperl version 1.0.1, and perl
> version 5.6.1 on Linux.
>
> Thanks,
> Hadas.
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu