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

Michael Gore mag87 at cornell.edu
Sat Jan 27 14:19:25 EST 2007


Chris,

Both versions of Perl and BioPerl on my machine were antiquated.

Problem solved with updates.

Thanks,

Mike 

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Saturday, January 27, 2007 9:35 AM
To: Michael Gore
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] swissprot stream with no ID. Not swissprot in my
book

This did fix it for most users; this is the first problem I have seen  
with it since then.

We don't have enough information to go on here to really diagnose the  
problem beyond that you're using Bio::Perl.  Are you using the latest  
BioPerl version (1.5.2, which has the fix)?  How did you retrieve  
your sequence (i.e. do you have a script)?  What OS are you on?

I run the following using the latest bioperl and it works:

use Bio::Perl;
my $seq = get_sequence('swissprot',"ROA1_HUMAN");
print $seq->accession_number,"\n";
print $seq->seq,"\n";

Chris

On Jan 27, 2007, at 1:27 AM, Michael Gore wrote:

> 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
>
>
>
> Office: (607) 255-1809
>
> Fax: (607) 255-6249
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







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