[Bioperl-l] problem

Scott Cain cain at cshl.edu
Thu Dec 21 08:56:21 EST 2006


Hello,

It looks to me like you have a networking problem that doesn't have
anything to do with BioPerl.  When I run your script, I get:

Bio::Seq::RichSeq=HASH(0x97013e0)

Fairly quickly, too.  Can you get to http://eutils.ncbi.nlm.nih.gov/ in
a browser without proxy settings?

As an aside, you probably don't really want the HASH stuff above, so I
modified your script to look like this, with warnings and strict to make
future debugging easier:

#!/use/bin/perl -w
use strict;

use Bio::DB::GenBank;

my $gb = new Bio::DB::GenBank;
my $seq1 = $gb->get_Seq_by_id('MUSIGHBA1');
print $seq1->seq;


Scott


On Thu, 2006-12-21 at 14:22 +0800, Somil Sharma wrote:
> hello
> 
> *i  run this program*
> 
> *#!/use/bin/perl*
> 
> *use Bio::DB::GenBank;*
> 
> *$gb = new Bio::DB::GenBank;
> $seq1 = $gb->get_Seq_by_id('MUSIGHBA1');
> print $seq1;
> *
> 
> *and got this error on cmd line--*
> 
> ---------- *EXCEPTION  -------------
> MSG: WebDBSeqI Request Error:
> 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (connect: Unknown error)
> Content-Type: text/plain
> Client-Date: Thu, 21 Dec 2006 06:28:33 GMT
> Client-Warning: Internal response*
> 
> *500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (connect: Unknown error)*
> 
> *STACK Bio::DB::WebDBSeqI::_request C:/Perl/lib/Bio/DB/WebDBSeqI.pm:685
> STACK Bio::DB::WebDBSeqI::get_seq_stream C:/Perl/lib/Bio/DB/WebDBSeqI.pm:491
> STACK Bio::DB::WebDBSeqI::get_Stream_by_id
> C:/Perl/lib/Bio/DB/WebDBSeqI.pm:27
> STACK Bio::DB::WebDBSeqI::get_Seq_by_id C:/Perl/lib/Bio/DB/WebDBSeqI.pm:145
> STACK toplevel C:\Perl\a2.pl:5*
> 
> plz see if u can help me out.
> 
> my ppm is also not able to install Bioperl so i did that also manually.
> 
> waiting for ur reply
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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