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

[Ewan Birney]

On Mon, 3 Jul 2000, Jason Stajich wrote:

> 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.

This is cruft - Bio::Seq::accession should be shot.

> 
> 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/
> 
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