[BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not
markw at illuminae.com
Fri Jan 9 16:09:04 EST 2004
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.
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 :-)
> 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>
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