[Bioperl-l] Bio::Tools::GFF GFF3 parsing

[Chris Mungall]

The main thing it seems to be missing is use of the ID and Parent tags to
indicate the relationship of features to one another.

I'm not really sure how best to do this, as this requires generating a
unique identifier for any feature that contains other features. The code
on the freaky-dev branch had a way of dealing with this, didn't it? I seem
to recall this would require some big changes to the core model.

Otherwise it looks great!

On Fri, 26 Sep 2003, Lincoln Stein wrote:

> Hi Jason,
>
> This is very good and I'm looking it over now.  Does it handle the CIGAR lines
> for gapped alignments?
>
> Lincoln
>
> On Thursday 18 September 2003 07:02 pm, Jason Stajich wrote:
> > I added support for GFF3 parsing to Bio::Tools::GFF and added some simple
> > tests.  I'm not 100% I have GFF3 output correct so Chris Mungall, Lincoln
> > if you don't mind giving it a look over that would be great.  If I've
> > duplicated functionality from somewhere else let me know, but I think
> > Bio::Tools::GFF needs to be able to parse in GFF3 format at some point.
> >
> > The GFF3 parsing seems to work fine for processing the BGDP annotations so
> > I feel confident it is working correctly, but more testing is welcomed!
> >
> > This is no real support for Unicode type output, the simpliest solution
> > would be to rely on HTML::Entities for encoding non-ASCII codes.  I wasn't
> > sure I wanted to make Tools::GFF depend on this right now so I've just
> > implemented a simple encoding for '=,;'.  Feel free to fix this if it
> > needs to be more aggresive.
> >
> > -jason
>
>