[Biopython-dev] Bio.GFF and Brad's code

[Peter]

On Tue, Dec 8, 2009 at 2:15 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>
>> There are other annoyances with the current SeqFeature
>> and FeatureLocation model - the strand and location operator
>> are part of the SeqFeature not the FeatureLocation. It would
>> make more sense to me to move them to the FeatureLocation
>> (and have that handle joins itself). Or, move everything to
>> the SeqFeature (and get rid of the FeatureLocation object).
>>

In addition to the strand and location operator, there is also
(sometimes) a database cross reference (properties ref and
db_ref, e.g. in contig files). Again, this is conceptually part
of the feature location (and stored that way in BioSQL if I
recall correctly).

One example of where it would make sense to move things
like the database, operator and strand to the FeatureLocation
is the coded_by information in some GenPept file annotation,
a use case very recently raised on the main mailing list:
http://lists.open-bio.org/pipermail/biopython/2009-December/005910.html
The current FeatureLocation simply can't be used here -
although a full SeqFeature could be.

Peter