[Bioperl-l] Re: Error using Bio::DB::SwissProt

[Anand Venkatraman]

>From: "Susan J. Miller" <sjmiller at email.arizona.edu>
>Subject: [Bioperl-l] Error using Bio::DB::SwissProt
>To: bioperl-l at portal.open-bio.org
>Message-ID: <418C125B.2000006 at email.arizona.edu>
>Content-Type: text/plain; charset=us-ascii; format=flowed

>When I run this small script:
> ---------------------------------------
> #!/usr/local/bin/perl -w
> use Bio::DB::SwissProt; 
> $sp = Bio::DB::SwissProt->new(); 
> $seqObj = $sp->get_Seq_by_acc('Q10654'); print $seqObj->display_id() . "\n";
> ---------------------------------------
> I see the error message:

> Use of uninitialized value in substitution (s///) > at  /usr/local/lib/perl5/site_perl/5.6.0/Bio/SeqIO/swiss.pm line 855,  <STREAM> line 30.

> The get_Seq_by_acc works, but I would like to present this to a class  and not have 
> the error message show up.  Any suggestions?

That is actually not an error....it is just a warning. 
 
That warning comes because the given accession "Q10654" is having a line starting with RG (instead of RA) around line 27. The next release of bioperl should fix this...
 
Try a different accesion num (Q15375)  in your script & you should not get those warnings.
 
Here is an extract from the Uniprot User manual (on the RA/RG lines) 
 
http://us.expasy.org/sprot/userman.html#Ref_line
-----------------------------------------------------------------------------------------------------------------------
3.10.6. The RA line

The RA (Reference Author) lines list the authors of the paper (or other work) cited. The RA line is present in most references, but might be missing in references that cite a reference group (see RG line). At least one RG or RA line is mandatory per reference block.

------------------------------------------------------------------------------------------------------------------


Anand
 
> Thanks,
>  -susan


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