[Bioperl-l] Bio::PrimarySeq and Selenocysteine

[Heikki Lehvaslaiho]

I added selenocysteine into the list of known amino acids.

	-Heikki

On Tue, 2003-07-22 at 12:53, Lincoln Stein wrote:
> Sorry, I was misreading the error message.  The problem isn't in 
> Bio::PrimarySeq, but in Bio::Tools::SeqStats:
> 
> 	use Bio::PrimarySeq;
> 	use Bio::Tools::SeqStats;
> 	$seq = Bio::PrimarySeq->new('UABCDEFGHIJ');
> 	$stats = Bio::Tools::SeqStats->new($seq);
> 
> ------------- EXCEPTION  -------------
> MSG:  Alphabet not OK for Bio::PrimarySeq=HASH(0x85a7c34) 
> 
> STACK Bio::Tools::SeqStats::_is_alphabet_strict 
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/SeqStats.pm:677
> STACK Bio::Tools::SeqStats::new 
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/SeqStats.pm:358
> STACK (eval) (eval 24)[/usr/local/lib/perl5/5.6.1/perl5db.pl:1521]:2
> STACK DB::eval /usr/local/lib/perl5/5.6.1/perl5db.pl:1521
> STACK DB::DB /usr/local/lib/perl5/5.6.1/perl5db.pl:1399
> STACK toplevel -e:1
> 
> Lincoln
> 
> On Tuesday 22 July 2003 06:49 am, Heikki Lehvaslaiho wrote:
> > Lincoln,
> >
> > How did you manage to get that error?
> > This works for me:
> >
> > #----------------------------------------------
> > use Bio::PrimarySeq;
> > $seq = Bio::PrimarySeq->new
> >     (-seq              => 'UABCDEFGHIJKLMN',
> >      -display_id       => 'new-id',
> >      -alphabet         => 'protein',
> >      -verbose          => 2);
> > $seq->seq('ABCDEFGHIJKLMNU');
> > #----------------------------------------------
> >
> > 	-Heikki
> >
> > On Mon, 2003-07-21 at 20:51, Lincoln Stein wrote:
> > > Hi,
> > >
> > > I guess I'm missing something.  I'm trying to load a protein that
> > > contains a selenocysteine (code "U") and am getting an exception about
> > > the protein alphabet not being right.  Is there an alternative alphabet
> > > that I should be using?
> > >
> > > Lincoln
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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