[Bioperl-l] bp_fetch.pl genbank example doesn't work anymore

Jason Stajich jason.stajich at gmail.com
Thu Sep 13 18:33:53 EDT 2012


Rob - that accession does not exist, but it works with a valid accession, what would you like it to do when the accession is not loadable?

perl scripts/index/bp_fetch.pl net::genbank:JX295726.1

On Sep 13, 2012, at 11:42 AM, Robert Buels <rbuels at gmail.com> wrote:

> Sigh.
> 
> rob at x bioperl-live$ perl -I. scripts/*/bp_fetch.pl net::genbank:X47072
> Sequence X47072 in Database genbank in net::genbank:X47072 is not loadable. Skipping.
> 
> Error
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: id 'X47072' does not exist
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
> STACK: Bio::DB::WebDBSeqI::get_Seq_by_id Bio/DB/WebDBSeqI.pm:167
> STACK: scripts/index/bp_fetch.pl:307
> -----------------------------------------------------------
> Sequence X47072 in Database genbank in net::genbank:X47072 is not loadable. Skipping.
> 
> Error
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: WebDBSeqI Request Error:
> HTTP/1.1 400 Bad Request
> Cache-Control: private
> Connection: close
> Date: Thu, 13 Sep 2012 18:40:49 GMT
> Server: Apache
> Content-Type: text/plain; charset=UTF-8
> Access-Control-Allow-Origin: *
> Client-Date: Thu, 13 Sep 2012 18:40:49 GMT
> Client-Peer: 165.112.7.20:80
> Client-Response-Num: 1
> Client-Transfer-Encoding: chunked
> NCBI-SID: 73BF4D7E05228B11_0006SID
> Set-Cookie: ncbi_sid=73BF4D7E05228B11_0006SID; domain=.nih.gov; path=/; expires=Fri, 13 Sep 2013 18:40:49 GMT
> 
> Cannot process ID list: OUT OF RANGE. Parameter retstart=0 + 1 is greater than number of IDs supplied in request. Incoming request includes 0 IDs.
> 
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
> STACK: Bio::DB::WebDBSeqI::_stream_request Bio/DB/WebDBSeqI.pm:773
> STACK: Bio::DB::WebDBSeqI::get_seq_stream Bio/DB/WebDBSeqI.pm:467
> STACK: Bio::DB::WebDBSeqI::get_Stream_by_id Bio/DB/WebDBSeqI.pm:288
> STACK: Bio::DB::WebDBSeqI::get_Seq_by_id Bio/DB/WebDBSeqI.pm:158
> STACK: scripts/index/bp_fetch.pl:307
> -----------------------------------------------------------
> 
> 
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




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