Database access for EMBOSS

[Peter Rice]

David Martin wrote:
> 
> On Mon, 20 Aug 2001, Peter Rice wrote:
> > For example, if your script is called 'remotegetz' just add this to the
> > database definition:
> >
> > app: remotegetz
> 
> This would then allow one to add whichever script one wanted as long
> as it could parse srs style arguements..
> 
> It doesn't have to be SRS, just look like it.. The potential is there
> for wrapping in house rdbms with such a script.
> 
> I'll add some more comments to the admin guide if Peter can send me
> details of how EMBOSS calls the wgetz program (not being much of an srs
> hacker myself).

This is getz, not wgetz. It supports the full SRS query language because it
calls getz (or a user defined script) with an SRS query constructed from
the USA.

But there is also an access method in general for external applications.
You can use this to set up RDBMS calls - which anyway was the original
intention.

At present it picks up dbname:id or dbname:acc as the rest of the command
line, or puts the id/accession into a formatted string (if the application
definition includes %s), but can easily be adapted further.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723