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

Chris Fields cjfields at uiuc.edu
Thu Oct 5 10:06:50 EDT 2006


On Oct 5, 2006, at 8:21 AM, Sendu Bala wrote:

> Marc Weimer wrote:
> [snip]
>>   my $db_obj = new Bio::DB::SwissProt(-verbose=>1);
>>
>>   my $seq_obj = $db_obj->get_Seq_by_acc('P43780');
> [snip]
>> using Bioperl 1.4-1 I get the error message
> [snip]
>>   ------------- EXCEPTION: Bio::Root::Exception -------------
>>   MSG: swissprot stream with no ID. Not swissprot in my book
> [snip]
>> Any suggestions?
>
> It works with the latest Bioperl. I'm not sure if 1.5.1 works (the  
> most
> recent official release), but 1.5.2 does
> (http://bioperl.org/wiki/Release_1.5.2), as does a checkout from CVS
> (http://bioperl.org/wiki/Getting_BioPerl#CVS).

Mark, you'll have to update to 1.5.2 or CVS, as Sendu suggested.   
There were server changes for biofetch which were fixed about 4-6  
months ago (post rel. 1.5.1); I think several changes were made to  
Bio::SeqIO::swiss as well during this period.

I think the error here results from Bio::SeqIO::swiss trying to parse  
an empty byte stream.  Sendu, do you think that Bio::SeqIO::swiss  
(and other SeqIO parsers) should throw a more specific message for  
getting an empty byte stream?  Or is it more trouble than it's worth?

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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