[Bioperl-l] Bio::DB::SeqFeature::Store delete() not working

Cook, Malcolm MEC at stowers-institute.org
Wed Jan 31 14:54:42 UTC 2007


I too have found the same to be true, traced the code, couldn't explain
to myself where lies the bug, and found through experimentation  that a
loop will get around it.  Causing me to write code such as:

      $gene->object_store->delete($_) foreach $gene->MRNA; # TODO:
understand why calling ->delete() only deletes 1 feature (not all)!


Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Wednesday, January 31, 2007 5:10 AM
> To: bioperl-l
> Subject: [Bioperl-l] Bio::DB::SeqFeature::Store delete() not working
> Hi,
> I'm trying to use Bio::DB::SeqFeature::Store delete() on a list of 
> Bio::SeqFeature::Annotated retrieved from the database. It 
> doesn't work. 
> I presume I'm falling foul of the issue pointed out in the docs:
> "WARNING: The current DBI::mysql implementation has some issues that
> need to be resolved, namely (1) normalized subfeatures are NOT
> recursively deleted; and (2) the deletions are not performed in a
> transaction."
> Is there a trick to avoid the problem? Or, how might someone go about 
> improving the implementation so that it worked?
> Cheers,
> Sendu.
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> Bioperl-l at lists.open-bio.org
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