[BioSQL-l] Re: [Biojava-l] _removeSequence

[Richard HOLLAND]

There is also the BS-zap-all script in the BioSQL distribution which
will wipe the whole lot for you in one go. :)

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biosql-l-bounces at portal.open-bio.org 
> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> mark.schreiber at novartis.com
> Sent: Monday, June 20, 2005 6:07 PM
> To: Martina
> Cc: biojava-l-bounces at portal.open-bio.org; BioJava; 
> biosql-l at open-bio.org
> Subject: [BioSQL-l] Re: [Biojava-l] _removeSequence
> 
> 
> To remove the database completely (while still keeping the 
> tables etc) you 
> would again need to turn on cascading deletes and delete the 
> appropriate 
> biodatabase row from the biodatabase table (or all of them if 
> you have 
> more than one).
> 
> You cannot currently do this using the biojava interface. You 
> would need 
> to code a JDBC statement to do it for you, or connect to the 
> DB and issue 
> the SQL statement yourself.
> 
> - Mark
> 
> 
> 
> 
> 
> Martina <boehme at mpiib-berlin.mpg.de>
> Sent by: biojava-l-bounces at portal.open-bio.org
> 06/20/2005 05:43 PM
> 
>  
>         To:     biosql-l at open-bio.org, BioJava <biojava-l at biojava.org>
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] _removeSequence
> 
> 
> Hi,
> 
> Im trying to delete a sequence and recursivly all its features.
> 
> So:
> 
> for (SequenceIterator si = db.sequenceIterator(); si.hasNext();) {
>                  Sequence s = si.nextSequence();
>                  String name = s.getName();
>                  s = null;
>                  db.removeSequence(name);
> }
> 
> But if I look in the database (MySQL  4.1.12) I can still see plenty 
> of entries and I have problems entering the same features again, 
> because of dublicate key error. I would like to know if 
> _removeSequence(String) in BioSQLSequenceDB is supposed to remove 
> features recursivly or just the features of the removed sequence?
> If so - what is the best way do delete the features of the features 
> (and so on)? And how to empty the db completly?
> 
> Martina
> 
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