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

[Jason Stajich]

heh - not yet.  I need to see whether we can use any of the existing cigar
parsing capabilities in Bioperl - either way I'd like to make this part
a Factory outside of Tools::GFF.  Pass in a cigar string get out
the appropriate feature representation (SimilarityPair or Search::HSP) or
pass in a SimilarityPair and get out the appropriate cigar string.

-jason

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
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu