[Bioperl-l] Re: primary_seq

[Ewan Birney]

On Mon, 2 Oct 2000, Hilmar Lapp wrote:

> 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
> branch.

great.

> 
> > 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?


I think wiki is the place for this.


We have had more of these problems with Ensembl and I my mind I think
there is the start of a sort of "coupling" paradigm which is somewhat
event-focused.


This event-style coupling allows modules to be used in standalone fashion
or coupled together and then work cleanly. I guess I should put forward a
proposal ;)




 > 
> 	Hilmar
> 
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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