[Bioperl-l] Question: creating an empty Bio::Seq object

[Scott Cain]

Hilmar,

Yep, the hash ref contains the right stuff.  While I have the current
checkout of bioperl, it is not in my @INC, and I can't seem to answer
the relatively simple question "what version am I using?", so I will
assume that it is too old, and install a newer version.

Thanks,
Scott


On Mon, 2002-12-02 at 11:59, Hilmar Lapp wrote:
> I checked it. It does work for me (perl 5.6.0, bioperl current checkout). Are you sure your hash contains the right stuff?
> 
> 	-hilmar
> 
> > -----Original Message-----
> > From: Scott Cain [mailto:cain@cshl.org]
> > Sent: Monday, December 02, 2002 7:49 AM
> > To: bioperl-l@bioperl.org
> > Subject: [Bioperl-l] Question: creating an empty Bio::Seq object
> > 
> > 
> > Hello all,
> > 
> > I have a relatively simple question.  I want to create a 
> > Bio::Seq object
> > before I have the actual DNA sequence, but when I do know the 
> > length, so
> > I would like to do something like this:
> > 
> > my $bioseq = Bio::Seq->new ( -alphabet         => 'dna'
> >                              -accession_number => $name ,
> >                              -length           => 
> > $$hash_ref{'seqlen'});
> > 
> > however, this doesn't appear to work.  Amusingly, if I do 
> > this and then
> > do $bioseq->length, it answers with '9', since the test 
> > accession number
> > I am using is 9 characters long (at least I assume that is where the 9
> > is coming from). So, is there a way to construct a Bio::Seq 
> > and give it
> > a length without actually having a DNA sequence?
> > 
> > Thanks,
> > Scott
> > 
> > 
> > -- 
> > --------------------------------------------------------------
> > ----------
> > Scott Cain, Ph. D.                                         
> > cain@cshl.org
> > GMOD Coordinator (http://www.gmod.org/)                     
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain@cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory