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

[Mark Wilkinson]

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