[Bioperl-l] UCSC database backend

Sendu Bala bix at sendu.me.uk
Thu Aug 10 02:56:59 EDT 2006

Sean Davis wrote:
> I have put together a variation of the database backend.  It is based on
> DBIx::Abstract and exposes a bit more of the SQL and DBI.  Since UCSC uses
> cross-database queries, it might be a better fit for the problem than an
> ORM.  It is pretty simple, but I don't know that we need much more here.
> The harder problem, as I mentioned earlier, is to determine what to return,
> not how to return it.  I am showing only a couple of the DBIx::Abstract
> methods here; there are a number of others for fetching data.  In
> particular, pretty much any of the fetch_* are available.

Seems to be reasonable so far. You could probably use the 
'introspection' calls to build other access methods on-the-fly.

>        A fair bit of work on the connection end.  In particular, I will
> proba-
>        bly make a "Bio::DB::SQL" class that encapsulates some methods for
>        working with SQL databases and some kind of abstraction for
> connection
>        information, making it easier to switch from local to remote versions
>        of a database.

That sounds really interesting.

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