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

Fields, Christopher J cjfields at illinois.edu
Fri Sep 14 16:23:10 EDT 2012


Should the script try to retrieve 0 IDs?  That seems like a bug.

chris

On Sep 14, 2012, at 2:57 PM, Robert Buels <rbuels at gmail.com> wrote:

> Well, two things then:
> 
> 1. the POD example should be updated to one that obviously works (I did this just now, https://github.com/bioperl/bioperl-live/commit/e59237909386e672f8b0e22004cc5e4196221321)
> 
> 2. It would be nice to translate NCBI's useless error message to something intelligible.
> 
> I'll settle for number 1 for now though.
> 
> R
> 
> On 09/13/2012 06:33 PM, Jason Stajich wrote:
>> 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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