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

Mark Wilkinson markw at illuminae.com
Fri Jan 9 15:45:10 EST 2004

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:


whereas I think I should be getting


In addition, it passes through all sorts of other tags that begin with 
capital letters:  


these should be


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 ;-) )



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