[Bioperl-l] circular refs/ unattach_seq in SeqFeatureI

[Jason Stajich]

Okay - it could have been some issues with my script too - I think I was
initially calling $feature->attach_seq($seq) instead of
$seq->add_SeqFeature($feature) which may do a better job keeping track of
things.

I was just trying to extract out sequences from annotated coding regions.
I'll see if I can't put together a use case that repeats the bug (sort of
makes the machine unusable when it gets to the mem problem though...).

-jason
On Fri, 24 Jan 2003, Ewan Birney wrote:

>
>
> On Thu, 23 Jan 2003, Jason Stajich wrote:
>
> > I propose adding a method unattach_seq to SeqFeatureI to allow one to
> > insure that no circular references exist for a seqfeature which attached
> > to a sequence. I am worried that memory is not be freed for Sequences
> > which have features attached when I was doing some iterations with
> > sequences that came from a Bio::Index::Fasta and then had features
> > attached and the memory allocation blew up on me.   Anyone else had
> > similar experiences?
> >
>
> In theory Bio::SeqFeature should be attached to the Bio::PrimarySeq so no
> circular references are in there, but that might not be happening...
> hmmm...
>
>
>
> I have no beef with unattach features, but I am worried that something
> else is screwed up elsewhere. I will poke around a bit...
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu