[BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not
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
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
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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