[Genquire-users] config files for data sources

[David Block]

On Tue, 13 Nov 2001, Brian Haas wrote:

> 
> Dave,
> 
> Is there a way to have the software work off of flatfiles, at least
> initially?

There was, and then we fixed it. :)

Genotator works off of flat files.  SeqCanvas works from flat files, via 
bioperl.  Genquire immediately puts things into a database - until someone 
writes a flat-file adaptor, I'm afraid you're stuck with MySQL.

Mark - do you have any suggestions?


Brian - Genquire was set up so that it's fairly easy to import data from 
fasta files for sequence and GFF files for features.  Unfortunately, the 
import routines may be broken because of some late schema changes.

If you can get you data files into some kind of bioperl-friendly format, 
bioperl will export things as gff.  Mark can help with that.

I am about to do a massive import of data into a local database - I'll 
keep you up-to-date with bugfixes, etc.

Thanks for keeping at it - I hope it works for you soon!


> 
> -Brian
> 
> 

-- 
David Block
GNF http://www.gnf.org  La Jolla, California
dblock@gnf.org        Let's not talk about the weather...