[BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly

[Mark Wilkinson]

Cool.  I'm heavily into making the HSP's output proper GFF3 today for
some of the Gbrowse tools that I have been working on, so I will jump in
and do this over the next day or two.

Cheers!

Mark

On Fri, 2004-01-09 at 14:49, Scott Cain wrote:
> I think everything you wrote below is correct.  As far as I know, only
> Allen and I have been working BTGFF's GFF3 code, and we haven't touched
> the alignment portion, so I am not surprised that it is wrong.  I
> suppose fixing BTGFF may break some tools, but I know that the chado
> loader I wrote will handle it correctly :-)
> 
> Thanks,
> Scott
> 
> 
> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote:
> > On Fri, 2004-01-09 at 11:22, Scott Cain wrote:
> > 
> > >   - be sure to use a SO term for the type (ie, match or one of its
> > > children)
> > 
> > So... actually the existing implementation of GFF3 in bioperl 
> > from Bio::Tools::GFF->new(-gff_version => 3)
> > does not generate correctly formatted GFF3 for alignment features, yeah?  
> > 
> > e.g. for column 9 of an alignment feature I get:
> > 
> > 	Target=gi|2828774:54232..54206
> > 
> > whereas I think I should be getting
> > 
> > 	Target=gi|2828774+54232+54206
> > 
> > In addition, it passes through all sorts of other tags that begin with 
> > capital letters:  
> > 
> > 	Bits=46.1;FracId=0.962962962962963
> > 
> > these should be
> > 
> > 	bits=46.1;fracId=0.962962962962963
> > 
> > if I am reading the spec correctly.
> > 
> > Finally, the column-3 term that comes out is "similarity", but it should be
> > one of the *match terms.  Is that also correct?
> > 
> > Please confirm that I am interpreting the GFF3 spec correctly for these
> > Alignment features and I would be happy to go in and fix things (a.k.a. break
> > everyone else's tools ;-) )
> > 
> > Cheerio!
> > 
> > Mark
> > 
-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae