[Bioperl-l] error when doing example 1.2

[Jason Stajich]

If the firewall is the problem you will need to configure the proxy first
- luckily we're using LWP so this is easy.  Obviously you need to put
something sensible in for http://myproxy .  To get more information read
the documentation for Bio::DB::WebDBSeqI and LWP and look for
documentation on the proxy method.

use Bio::DB::SwissProt;
my $database = new Bio::DB::SwissProt;

$database->proxy(['http','ftp'], 'http://myproxy');
my $seq = $database->get_Seq_by_id('BACR_HALHA');
print "Seq: ", $seq->accession_number(), " -- ", $seq->desc(), "\n\n";

-jason
On Tue, 29 Jan 2002, Lihn, Horng-Twu wrote:

> I have a newbie question. I am going through example 1.2
>
> use Bio::DB::SwissProt;
> my $database = new Bio::DB::SwissProt;
> my $seq = $database->get_Seq_by_id('BACR_HALHA');
> print "Seq: ", $seq->accession_number(), " -- ", $seq->desc(), "\n\n";
>
> And get the following error. What does it mean?
> Is it the problem of the remote server or the problem with
> my company's firewall setting. How do I overcome this?
>
> --Steve
>
>
> -------------------- WARNING ---------------------
> MSG: 500 (Internal Server Error) Can't connect to www.ebi.ac.uk:80 (Timeout)
> Client-Date: Tue, 29 Jan 2002 19:15:55 GMT
>
>
>
> ---------------------------------------------------
> -------------------- EXCEPTION --------------------
> MSG: WebDBSeqI Request Error
>
> STACK Bio::DB::WebDBSeqI::_request C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:446
> STACK Bio::DB::WebDBSeqI::get_seq_stream
> C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:298
> STACK Bio::DB::WebDBSeqI::get_Stream_by_id
> C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:196
> STACK Bio::DB::WebDBSeqI::get_Seq_by_id
> C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:139
> STACK toplevel exam1.2.pl:5
> -------------------------------------------
>
>
>   Steve Lihn
>   Merck & Co., Inc.
>   Tel: (908) 423 - 4441
>
>
>
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>

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