[Bioperl-l] Bio::PrimarySeq and Selenocysteine

[Lincoln Stein]

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

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)