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

Matthew Pocock mrp@sanger.ac.uk
Tue, 20 Feb 2001 13:00:02 +0000

> I'm not sure but I think the historic gff_string() wouldn't parse
> truely GFF2-compliant strings correctly. Is that right Mark?
> (otherwise we wouldn't need _from_gff2_string())
> So, your point leads to the question whether to have one single
> _from_gff() that gracefully parses GFF1, bad GFF, and GFF2, or
> have _from_gff2 and _from_gff1. The first option seems prone to
> cause nightmares. Comments? Mark?
> 	Hilmar

<heresy>Could you not produce a GFF module that looks very similar to 
the SeqIO stuff that consumes text and is a factory for features? It can 
also have the methods for producing GFF. GFF is a file format, and is in 
no way integral to SeqFeatureI.</heresy>