[Bioperl-l] GFF method in Bio::SeqFeatureI

[Ewan Birney]

On Fri, 16 Feb 2001, Hilmar Lapp wrote:

> There now two methods in SeqFeatureI for every gff-concerned
> operation: gff_string() and gff2_string(), _from_gff_string(),
> _from_gff2_string(), and two named parameters in new().
> 
> Inheriting classes all use gff_string() and friend.
> 
> I suggest we remove the old implementation of gff_string() and
> rename Mark W.'s gff2_string() to the former. Likewise for the
> other methods.
> 
> Alternatively, we rename gff_string() to gff1_string(), and
> gff2_string() to gff_string().
> 
> I prefer the first option. Any objections?

I am good with outputting only gff2, but we need to accept gff1 - or
indeed badly formatted gff in general. If I remeber rightly, Mark's
_from_gff2_string is very "picky" whereas there is alot of "GFF" out there
which is no where near the spec.



 > 
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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