[Bioperl-l] Re: Bioperl-l Digest, Vol 21, Issue 1

[Scott Cain]

Hi Hilmar,

SeqFeature::Annotated (which is what FeatureIO::gff is using) has a
score method that stores the score as a Annotation::SimpleValue, which
means it is used like this:

  my $score = $feature->score->value;

which seems to work well for GFF3 (since scores are by definition a
single value in GFF3).

Scott


On Mon, 2005-01-03 at 10:51 -0500, bioperl-l-request at portal.open-bio.org
wrote:
> Date: Sun, 2 Jan 2005 16:28:52 -0800
> From: Hilmar Lapp <hlapp at gnf.org>
> Subject: [Bioperl-l] score in seqfeature
> To: Allen Day <allenday at ucla.edu>, Bioperl <bioperl-l at bioperl.org>
> Message-ID: <71B3DC9D-5D1E-11D9-827C-000A959EB4C4 at gnf.org>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
> 
> Allen et al, what are the (GFF3-driven?) plans for storing the score 
> property introduced by SeqFeature::Generic?
> 
> The reason I'm asking is that it doesn't get (de-)serialized in 
> bioperl-db because it's neither defined on SeqFeatureI nor has it been 
> internal stored as a tag/value pair. I'd like to fix this issue, either 
> by pulling it into the annotation bundle in 
> SeqFeature::AnnotationAdapter, or by some other means that maybe is 
> friendlier or more useful to GFF3 minds.
> 
> 	-hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory