[Bioperl-l] Bio::DB:GFF

[Lincoln Stein]

Hi Oliver,

This is just a stupid omission from the API (I come from a background where 
data is never deleted from a database, but merely marked with an "obsolete" 
flag).  I'm happy to fix, since you're not alone in requesting this feature.  
Can you suggest the form of the calls that you'd like to use to do deletes 
and updates?

On a related note, the current bioperl CVS has an experimental 
fast_load_gff.pl script which makes incremental loading almost as fast as the 
bulk loader.

Lincoln

On Thursday 05 September 2002 09:01 am, Oliver Burren wrote:
> Hi,
>
> I'm currently looking at the excellent Generic Genome Browser to visualise
> some annotation we have in our lab. This has got me using Bio::DB::GFF
> which works well for the addition of GFF files into a MySQL db. However
> there seems to be no reciprocal provision for removing data from the
> database (i.e. if it is wrong or need updating). Currently I just go in
> and remove the data by hand using SQL. I was wondering if anyone has had
> any thoughts about methods that allow you to remove data from database
> using a Bio::DB:GFF object? For example 'remove all features contained in
> segment IDDM1 with a source of CDS'? Do these methods exist already and I
> just haven't found them ?
>
> Thankyou,
>
> Olly Burren
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-- 
Lincoln Stein
lstein@cshl.org