[Bioperl-l] Bio::EnsemblLite::UpdateableDB

[Jason Stajich]

Preliminary version of the module Bio::EnsemblLite::UpdateableDB is
checked in to bioperl (bioperl-db repository).

This just does basic stuff by talking to a mysql db server, add a Bio::Seq 
to the db, remove a seq, and fetch a seq from the db and make it into a
Bio::Seq object.  This had to be separate code with separate tables 
(from ensembl) because I am not expecting sequences to be part of contigs
at this time.

So there are a set of add-on tables to provide a seq description 
and an association of generic features to seqs.

sql/ensembl-lite-mysql-addon.sql - add ons
sql/ensembl-lite.sql - ensembl-lite code (only the dna table is really
                       used from this at present)

I have been trying to put the EnsemblLite spec that I will
propose on ensembl.org's wikki, but have been getting web errors.  (It
just KNOWS everyone is getting ready for summer holidays).  Will try again
over the weekend.  

short TODO list (lest you think this is really finished code being
                 submitted)

 - implement _update function for updating seqs
 - implement get_PrimarySeq_stream
 - table schema discussion with interested parties, it is not really
   CORRECT to refer to a table of sequences as 'dna' if some are protein
   seqs...  Include a graphical table schema on doc.
 - Start looking at the analysis pipline runnable/runnabledb system from
   Ensembl and how we can hook into it.

-Jason

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/