[Bioperl-l] $seq->accession vs accession_number

[Jason Stajich]

We have Bio::Seq::accession and Bio::Seq::accession_number (
which accesses Bio::PrimarySeq::accession_number).  But is there really
a need for these to be separate?  I expected to run a genbank parser and
get data in the $seq->accession_number field for a sequence, but instead
saw all unknowns.   Bio::SeqIO::genbank only uses $seq->accession so the
data was only accessible through that method.

Is this intentional?  Should they point to the same underlying storage
instead?  Bio::PrimarySeq::accession_number points to
$obj->{'accession_number'} while Bio::Seq::accession points to 
$obj->{'accession'}.

 Title   : accession_number
 Usage   : $unique_biological_key = $obj->accession_number;
 Function: Returns the unique biological id for a sequence, commonly
           called the accession_number. For sequences from established
           databases, the implementors should try to use the correct
           accession number. Notice that primary_id() provides the
           unique id for the implemetation, allowing multiple objects
           to have the same accession number in a particular
implementation.

           For sequences with no accession number, this method should
return
           "unknown".
 Returns : A string
 Args    : None

 Title   : accession
 Usage   : $obj->accession($newval)
 Function: Whilst the underlying sequence object does not 
           have an accession, so we need one here. Wont stay
           when we do the reimplementation.
 Example : 
 Returns : value of accession
 Args    : newvalue (optional)


-Jason

Jason Stajich
Center for Human Genetics
Duke University Medical Center
jason@chg.mc.duke.edu
(919)684-1806 (office)
(919)684-2275 (fax)
http://wwwchg.mc.duke.edu/