[Bioperl-l] Bio::DB::GenBank problem with get_Seq_by_acc

[Prachi Shah]

Hi,

While using the get_Seq_by_acc function with the
Bio::DB::GenBank module, I get the following error
with some accession numbers. It is not able to connect
to "www.ebi.ac.uk:80". The problem is that the code
exits with this error. It is ok for me if it cannot
find some sequences, but I want the code to ignore
this error and proceed. Is there a way to do that?

thanks,
Prachi.



-------------------- WARNING ---------------------
MSG: error in parsing a report:
 
not well-formed (invalid token) at line 3074, column
150, byte 169513 at
/home/pss11/Perl/XML-Parser-2.31/lib/site_perl/5.6.0/i386-linux/XML/Parser.pm
line 185

---------------------------------------------------
Num: 1  Query Accession BAC56945.1 

-------------------- WARNING ---------------------
MSG: [NP_572240] is not a normal sequence database but
a RefSeq entry. Redirecting the request.

---------------------------------------------------

------------- EXCEPTION  -------------
MSG: WebDBSeqI Request Error:
500 (Internal Server Error) Can't connect to
www.ebi.ac.uk:80 (Timeout)
Client-Date: Tue, 18 Feb 2003 15:26:19 GMT



STACK Bio::DB::WebDBSeqI::_stream_request
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:692
STACK Bio::DB::WebDBSeqI::get_seq_stream
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:423
STACK Bio::DB::NCBIHelper::get_Stream_by_acc
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0/Bio/DB/NCBIHelper.pm:412
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:172
STACK toplevel newidea.pl:337

--------------------------------------

------------- EXCEPTION  -------------
MSG: acc does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:176
STACK toplevel newidea.pl:337

--------------------------------------


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