[Bioperl-l] Bio::DB:GFF

[Marc Logghe]

It is excellent indeed.
Concerning your question: as far as I know these methods currently do not
exist. I had the same problem. I took backups between every major feature
entry and imported the gff files again with the appropriate changes in the
corresponding restored database.
A similar problem is eg. when you dump a segment object
(Bio::DB::GFF::RelSegment) using Bio::SeqIO
 you get *all* features on the segment. How do you remove the features you
don't want from the object before dumping ?
Marc 
> -----Original Message-----
> From: Oliver Burren [mailto:Oliver.Burren@cimr.cam.ac.uk] 
> Sent: Thursday, September 05, 2002 3:01 PM
> To: Bioperl-l
> Subject: [Bioperl-l] Bio::DB:GFF
> 
> 
> 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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