[Bioperl-l] How to check the validity of an accession number ?

[Heikki Lehvaslaiho]

Damien,

The change is in the bioperl code. It was put in almost 11 months ago
for the 1.2 release. As the error message indicates, line 177 in
Bio::DB::WebDBSeqI now throws an error. You can catch it with eval
statement, e.g:

  eval {
      $seq = $stream -> get_Seq_by_acc($an);
  }
  if ($@) {
      print STDERR "Not a valid accession [$an]\n";
      next;
  }


The Web interface to the bioperl CVS repository can help you track 
whys, whens and hows of code changes:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/DB/WebDBSeqI.pm?cvsroot=bioperl

Yours,

-Heikki


On Sat, 2003-11-08 at 05:02, Damien Marsic wrote:
> Hello,
> 
> I hope someone will be able to help. I wrote a program that does the
> following:
> 
> - opens a file containing sequences named with their Genbank accession
> number if it exists (and an arbitrary name if the sequence is not in
> Genbank)
> 
> - reads each sequence name, looks in Genbank if it is an accession number,
> and if it is, retrieves the organism name and other information. If the name
> is not recognized as an accession number, the program says it and proposes
> to continue with the next sequences.
> 
> My programs worked perfectly during the last 2 years or so. But for the last
> few months it does not work anymore, although I did not make any change to
> it. What is happening now is that when there is a sequence name that is not
> an accession number, the program crashes.
> 
> The problem lies with this line:
> 
>    $seq = $stream -> get_Seq_by_acc($an);
> 
> When $an was an invalid accession number, $seq used to be "undefined" and
> the program could go on (the program checks whether &seq in defined or
> undefined and then goes to the appropriate step).
> 
> But now, when $an is an invalid accession number, the program just crashes
> with the following message:
> 
>  ------------- EXCEPTION  -------------
>  MSG: acc does not exist
>  STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
>  /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:177
>  STACK Bio::DB::GenBank::get_Seq_by_acc
>  /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GenBank.pm:216
>  STACK toplevel phylplus.pl:90
>  --------------------------------------
> 
> Can someone helps me understand what is happening ? Were there some changes
> at Genbank that could explain why my program behaves differently ? Is there
> anything I can do to make it behave like it did before ?
> 
> Is there any other way than "get_Seq_by_acc" to check if an accession number
> exists or not ?
> 
> Thanks in advance for the replies.
> 
> Damien
> 
> 
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