[Bioperl-l] Request for comments: Bio::DB::GFF3 namespace

Lincoln Stein lstein at cshl.edu
Tue Mar 21 18:27:30 EST 2006


Hi All,

I'm pretty much ready to check in the replacement for the Bio::DB::GFF 
database. What I ended up writing has only a remote relationship to gff3 
files -- it is more like a general storage engine for Bio::SeqFeatureI 
objects. So I don't want to call the thing Bio::DB::GFF, but want to place it 
somewhere else in the namespace hierarchy.

Here are my current classes and what they do; the names are placeholders so 
don't get hung up on what they're called now:

	Bio::SeqFeature::Store
		- implements the Bio::SeqFeature::CollectionI interface. You can
		store any Bio::SeqFeatureI into a database (mysql, berkeleydb, in-memory)
		and fetch it out using a variety of queries.

	Bio::SeqFeature::Store::DBI
		- base class for DBI databases

	Bio::SeqFeature::Store::DBI::mysql
		- mysql storage implementation

	Bio::SeqFeature::Store::DBI::mysql::Iterator
		- helper class for the mysql adaptor. Implements 
			(part of) the Bio::SeqIO interface

	Bio::SeqFeature::Store::memory
		- in-memory storage implementation

	Bio::SeqFeature::Store::bdb
		- Berkeley DB storage implementation

	Bio::SeqFeature::Store::Cacher
		- An in-memory cache for the store; uses an LRU cache
			to avoid going to the database for frequently used
			objects. Also implements  scheme that lets features
			share the same in-memory subfeatures (like shared
			exons).

	Bio::SeqFeature::LazyFeature
		- A Bio::SeqFeatureI class that stores its subfeatures in an
			underlying Bio::SeqFeature::Store and fetches them
			in a lazy fashion as needed.

	Bio::SeqFeature::LazyTableFeature
		- A Bio::SeqFeatureI class that stores its subfeatures in
			an underlying Bio::SeqFeature::Store, AND stores
			the parent/child relationship data in the Store as
			well. Fetches subfeatures as needed in a lazy fashion.

A utility script, currently called gff3_load.pl, parses a gff3 file, creates 
the proper objects, and stores them in the Store. Eventually some of this 
functionality will be moved into Bio::Tools::GFF.

So where should I put these files? The Bio::DB namespace? A new 
Bio::Collection namespace? A Bio::SeqFeature::Collection namespace?

Lincoln


-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING, 
PLEASE CONTACT MY ASSISTANT, 
SANDRA MICHELSEN, AT michelse at cshl.edu (516 367-5008)


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