[Bioperl-l] Re: Proposed GFF version 3

[Ewan Birney]

> >     1) adds a mechanism for representing more than one level
> >        of hierarchical grouping of features and subfeatures.
> >     2) separates the ideas of group membership and feature name/id
> >     3) constrains the feature type field to be taken from a controlled
> >        vocabulary.
> >     4) allows a single feature, such as an exon, to belong to more than
> >        one group at a time.
> >     5) one level of relative addressing for subfeatures (e.g. exons
> >        can be expressed in transcript coordinates)

The only thing I worry about is (5). I would claim that the format will be
more useful if parsers and tools can assumme that all coordinates are in
one coordinate system - otherwise all your nice sort -k commands cant be
used.


Yup - I know - Ace plays nicely with the relative coordinates ;) I would
drop this though - you gain a far higher piece of utility with the dumping
code just having to do:

   print $exon->relative_start + $gene->start+1,"\n";

for the coordinate, which aint that hard.