[Bioperl-l] Re: score in seqfeature

[Hilmar Lapp]

So, what does this mean for SeqFeature::Generic's future? Any input or  
comments, e.g. from the people who've had opinions on that before?

	-hilmar

BTW the digest title as email subject sucks. Sorry.

On Monday, January 3, 2005, at 08:34  AM, Scott Cain wrote:

> 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
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------