[Bioperl-l] Bio::DB::SwissProt Error
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:
>> my $db_obj = new Bio::DB::SwissProt(-verbose=>1);
>> my $seq_obj = $db_obj->get_Seq_by_acc('P43780');
>> using Bioperl 1.4-1 I get the error message
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: swissprot stream with no ID. Not swissprot in my book
>> Any suggestions?
> It works with the latest Bioperl. I'm not sure if 1.5.1 works (the
> recent official release), but 1.5.2 does
> (http://bioperl.org/wiki/Release_1.5.2), as does a checkout from 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?
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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