[Bioperl-l] circular refs/ unattach_seq in SeqFeatureI

[Ewan Birney]

On Fri, 24 Jan 2003, Jason Stajich wrote:

> 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.

$feature->attach_seq($seq) is going to end in tears. You want to be going

$feature->attach_seq($seq->primary_seq());


<aside>why oh why doesn't Perl have a nice garbage collector. And when 
Perl 6 comes and Parrot does have one, will Perl 5 be "ported" to 
Parrot?</asode>

> 
> 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...).
> 


Hmmm... is there a piece of bioperl library code which is

$feature->attach_seq($seq)? anywhere. ...