[MOBY-l] new objects for sequence features

[Mark Wilkinson]

Hi MOBYers!

I needed to create some new Sequence/Feature objects in order to build
services to run OOTB on a Gbrowse installation.  These will no doubt be
useful to other people as these kinds of objects didn't exist up to now.

There is a hierarchy of GFF objects (GFF (root), GFF1, GFF2, GFF2_5,
GFF3) that you can use to pass GFF feature files as formatted text.  In
addition there is a BasicGFFSequenceFeature object that holds all of the
required GFF fields, along with an indeterminate number of key/value
pair objects.  These Key/value pair objects are also new, and come in
two flavours:  simple_key_value_pair for 1:1 key/value relationships,
and multi_key_value_pair for 1:many key/value relationships, such as
exist in GFF & Ace.  Finally, there is a new DNA Sequence object
'DNASequenceWithGFFFeatures' which is a DNA sequence containing a
corresponding set of BasicGFFSequenceFeature objects.

have fun, and let me know if you think these objects are badly
conceived.

M

-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae