[Bioperl-l] MSG: acc does not exist, but acc is OK and bioperl version is 1.2.2

[Vince Forgetta]

Thanks a bunch ! Turns out that EBI doesn't have NM_003000, but NCBI 
does. I thought they were the same thing ! I'll just DL refseq from NCBI.

Vince

Jason Stajich wrote:

>You can see if it is the case by going to
>http://www.ebi.ac.uk/cgi-bin/dbfetch
>and plugging in your accession.
>
>refseq is available for download from ncbi site - you will find this
>faster and more reliable than most webbased sequence server I expect.
>
>-jason
>On Fri, 20 Feb 2004, Vince Forgetta wrote:
>
>  
>
>>I had originally put $accession without single quotes and got the same
>>error. I tried the single quotes as a debugging step. I still have the
>>same problem when I remove them.
>>
>>The problem seems to be sporadic. some days I can get accessions and
>>other days I run into problems. Could this be the problem:
>>
>>http://bioperl.org/Core/Latest/faq.html#Q2.3
>>
>>Thanks.
>>
>>Andreas Kahari wrote:
>>
>>    
>>
>>>On Fri, Feb 20, 2004 at 10:14:40AM -0500, Vince Forgetta wrote:
>>>[cut]
>>>
>>>
>>>      
>>>
>>>>------------- EXCEPTION  -------------
>>>>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:177
>>>>
>>>>My code is:
>>>>
>>>>  use Bio::DB::RefSeq;
>>>>  $gb = new Bio::DB::RefSeq;
>>>>  my $seq;
>>>>  $seq = $gb->get_Seq_by_acc('$accession');
>>>>
>>>>
>>>>        
>>>>
>>>Perl does not interpolate variables in within single quotes.
>>>You probably want to say
>>>
>>>   $seq = $gb->get_Seq_by_acc($accession);
>>>
>>>
>>>Cheers,
>>>Andreas
>>>
>>>
>>>
>>>      
>>>
>>
>>    
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>
>  
>


-- 
Vincenzo Forgetta

 Computational Biology
  McGill University and Genome Quebec Innovation Centre
  740 Dr. Penfield Avenue Room 7211
  Montreal, Quebec Canada, H3A 1A4

  Tel: 514-398-3311 00476 
  Email: vince.forgetta at staff.mcgill.ca