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

Robert Buels rbuels at gmail.com
Fri Sep 14 15:57:39 EDT 2012


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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