[Bioperl-l] circular refs/ unattach_seq in SeqFeatureI

[Jason Stajich]

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

Other than in Bio::Seq of course?

This was all in my own script, I think I was getting out Bio::PrimarySeq
from Bio::Index::Fasta (or so I assumed) -- these however could have been
Bio::Seq objects.  I then just attached the seq to the feature with
attach_seq.  Things seemed to behave better when I switched to
Bio::DB::Fasta for the indexing ( I thought initially that it was maybe
because DB::Fasta won't bring a seq into memory if you end up doing a
subseq).  Then I was attaching a feature on it, getting the spliced
sequence out from it, writing out the spliced seq, and then throwing
everything away.

-jason

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu