[Bioperl-l] acc does not exist

[Heikki Lehvaslaiho]

"Brent and Johnetta",

Brian just committed this change into the cvs repository.

Modified Files:
        NCBIHelper.pm 
Log Message:
The eutils base URL has changed to
http://eutils.ncbi.nlm.nih.gov/entrez/eutils

The change in the URL is probably the reason for the script failing.
This change will end up into 1.2.2 maintenance release, but you can
change it by hand for now in your copy of NCBIHelper.pm 

The error message is not too informative. Sorry about that.

	-Heikki

On Mon, 2003-06-09 at 02:19, Brent and Johnetta Smith wrote:
> I just recently installed BioPerl 1.2.1 on RedHat v9.0.  I'm trying to
> execute the bptutorial script:
> 
> #!/usr/bin/perl
>  
>   use Bio::Perl;
>  
>   # this script will only work with an internet connection
>   # on the computer it is run on
>  
>   $seq_object = get_sequence('genbank',"AF421111");
>  
>   write_sequence(">test.fasta", 'fasta', $seq_object) ;
>  
> and I receive the following error:
> 
> MSG: acc does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:176
> STACK Bio::Perl::get_sequence
> /usr/lib/perl5/site_perl/5.8.0/Bio/Perl.pm:510
> STACK toplevel bpTest.pl:10
>  
> I am absolutely 100% certain that the accession number exists on GenBank
> (I verified and re-verified several times by going directly to their web
> site).  Also, when "genbank" is changed to "swissprot" and a valid
> accession number for swissprot is put in place of the AF421111 then it
> works perfectly.  I have installed BioPerl on another RedHat 9.0
> computer and it was working with both swissprot and genbank last time I
> checked (last Tuesday).
> 
> Any suggestions?
> 
> Thank you.
> 
> Also, if this question is not appropriate for this list then please let
> me know where to go for a users list.
-- 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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