[Bioperl-l] Error message

Brian Osborne osborne1 at optonline.net
Tue Jun 20 12:13:51 EDT 2006


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
> 
> 
> 
> 
> 
> 
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