[Bioperl-l] Re: primary_seq

Hilmar Lapp hlapp@gmx.net
Mon, 02 Oct 2000 11:11:39 +0200

Ewan Birney wrote:
> > My concern here is also that the code doing this on either branch/trunk
> > is probably wrong, given the recent bug-fix in embl.pm (removal of
> > explicit creation of a PrimarySeq object). I'm wondering whether we
> > should scan all SeqIO modules for this potential bug and fix them all.
> > Ewan, what do you think.
> >
> We should scan for these explicit primary_seq makes. James and I were
> looking at this a couple of weeks ago and wondering how best to do things.

Done. It seems that swiss.pm was the only additional parser creating
primary_seq explicitely, and I fixed it on both the main trunk and the

> We have a *big* problem with desc as it is present both on primary_seq and
> annotation, and justifably on both. All very messy, but it seems to be
> main trunk stuff here.

Agreed. I think we should have a TODO list for such kind of stuff to be
kept in mind. Or is the Wiki the right place for it?


Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
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