[Bioperl-l] Bio::DB::SeqFeature::Store delete() not working
bix at sendu.me.uk
Wed Jan 31 09:47:03 EST 2007
Sendu Bala wrote:
> 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
> Is there a trick to avoid the problem? Or, how might someone go about
> improving the implementation so that it worked?
Actually, it was just a simple bug in
I've committed a fix that I hope won't break anything; all I did was
have it return the number of rows deleted, since
Bio::DB::SeqFeature::Store::delete() needs a true return from
_deleteid() or it will only delete the first feature supplied to it.
(I've left the current implementation for delete() which effectively
gives up the moment a feature fails to be deleted, instead of trying to
delete the remaining features it was supplied.)
I propose changing delete() to return the number of features it
successfully deletes instead of boolean, to match store() behaviour. But
that isn't so important.
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