[Bioperl-l] swissprot stream with no ID. Not swissprot in my book

[Michael Gore]

I am having a similar error retrieving sequence from SwissProt.  Thought may
be changing 'swall' to 'UniProtKB' would solve the issue, but it still
remains.
 
>>> ------------- EXCEPTION  -------------
>>> MSG: swissprot stream with no ID. Not swissprot in my book
>>> STACK Bio::SeqIO::swiss::next_seq /Library/Perl/5.8.6/Bio/SeqIO/
>>> swiss.pm:179
>>> STACK Bio::DB::WebDBSeqI::get_Seq_by_id /Library/Perl/5.8.6/Bio/DB/
>>> WebDBSeqI.pm:153
>>> STACK Bio::Perl::get_sequence /Library/Perl/5.8.6/Bio/Perl.pm:513
>>> STACK toplevel tut2.pl:5
 
 
It must be a URL issue?  Does anyone know a remedy?
 
New Bio-Perl User
 
Mike 
 
 
 
On 6/20/06 1:16 PM, "Chris Fields" <cjfields at uiuc.edu
<http://lists.open-bio.org/mailman/listinfo/bioperl-l> > wrote:
 
> Brian,
> 
> Brian,
> 
> Looks like EBI switched the url parameter for swissprot 'swall' to
> 'UniProtKB'.  I committed a change to Bio::DB::SwissProt in CVS which
fixes
> this and solves the issue.
> 
> Chris
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
<http://lists.open-bio.org/mailman/listinfo/bioperl-l>  [mailto:bioperl-l-
>> bounces at lists.open-bio.org
<http://lists.open-bio.org/mailman/listinfo/bioperl-l> ] On Behalf Of Brian
Osborne
>> Sent: Tuesday, June 20, 2006 11:14 AM
>> To: George Tzotzos; bioperl-l at lists.open-bio.org
<http://lists.open-bio.org/mailman/listinfo/bioperl-l> 
>> Subject: Re: [Bioperl-l] Error message
>> 
>> George,
>> 
>> The docs I'm reading say to use 'swiss', not 'swissprot' but I think
>> there's
>> some other problem that may be specific to SwissProt. Can you retrieve
>> from
>> GenBank? E.g.:
>> 
>> my $seq_object = get_sequence('genbank', 2);
>> 
>> Brian O.
>> 
>> 
>> On 6/20/06 7:36 AM, "George Tzotzos" <G.Tzotzos at unido.org
<http://lists.open-bio.org/mailman/listinfo/bioperl-l> > wrote:
>> 
>>> I'm a BioPerl novice. I used CPAN to install BioPerl and run the
>>> following script to test the installation:
>>> 
>>> use Bio::Perl;
>>> use strict;
>>> use warnings;
>>> 
>>> my $seq_object = get_sequence('swissprot', "P09651");
>>> 
>>> write_sequence(">roa1.fasta", 'fasta', $seq_object);
>>> 
>>> I used as argument both "ROA1_HUMAN" and "P09651". In both cases I
>>> get the message below.
>>> 
>>> Any help on the nature of the problem and how to overcome it would be
>>> greatly appreciated.
>>> 
>>> Thanks
>>> 
>>> George
>>> 
>>> 
>>> ------------- EXCEPTION  -------------
>>> MSG: swissprot stream with no ID. Not swissprot in my book
>>> STACK Bio::SeqIO::swiss::next_seq /Library/Perl/5.8.6/Bio/SeqIO/
>>> swiss.pm:179
>>> STACK Bio::DB::WebDBSeqI::get_Seq_by_id /Library/Perl/5.8.6/Bio/DB/
>>> WebDBSeqI.pm:153
>>> STACK Bio::Perl::get_sequence /Library/Perl/5.8.6/Bio/Perl.pm:513
>>> STACK toplevel tut2.pl:5
>>> 
>>> 
>>> 
>>> George T. Tzotzos Ph.D
>>> Vienna, Austria

 

 

Michael Gore

Graduate Student 

Department of Plant Breeding and Genetics  

Cornell University 

Institute for Genomic Diversity 

175 Biotechnology Building 

Ithaca, NY 14853-2703

 

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