[Bioperl-l] Error message

Chris Fields cjfields at uiuc.edu
Tue Jun 20 13:16:32 EDT 2006


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 [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Brian Osborne
> Sent: Tuesday, June 20, 2006 11:14 AM
> To: George Tzotzos; bioperl-l at lists.open-bio.org
> 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> 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
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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