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

[Jason Stajich]

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