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

Scott Cain cain at cshl.org
Fri Jan 9 15:49:17 EST 2004

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 :-)


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
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

More information about the Bioperl-l mailing list