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

[Allen Day]

We don't support this in the chado load_gff3.pl script, but it wouldn't be
very difficult to add handling of simple cases.  I am concerned though
about difficulties handling potential ambiguity wrt the strandedness of
relative coordinates.

I assume by relative coordinates here, you mean you're describing a
feature's position in terms of the position of another feature which is
itself described in absolute coordinates (or is relative to a feature
which is).

-Allen



On Fri, 9 Jan 2004, Aaron J.Mackey wrote:

> Hi Scott,
> 
> Thanks for the quick reply, but that wasn't exactly the nature of the  
> question; the question was whether (apart from Gap attributes), do  
> gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the  
> rest of GFF3, namely to provide the ability of input GFF3 with features  
> that aren't in absolute reference coordinates, but in relative  
> coordinates?  And is that ability in release 1.58, or some CVS branch I  
> can access (code that lives quietly in the depths of Lincoln's hard  
> drive doesn't count)?
> 
> Thanks,
> 
> -Aaron
> 
> On Jan 9, 2004, at 4:47 PM, Scott Cain wrote:
> 
> > OK, I am going to answer this, but if I am wrong, I'm sure Lincoln will
> > correct me.  I don't think gbrowse or BDGFF knows how to deal with  
> > cigar
> > lines in Gap attributes yet.  It is safer for the moment to continue to
> > put separate HSPs on separate GFF lines for the time being.
> >
> > Scott
> >
> >
> > On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote:
> >> Forgive me for a stupid question, but does GBrowse (v1.58) now support
> >> GFF3?  Namely, can I have start/stops in sub-feature coordinates in my
> >> input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate
> >> "canonical" top-level coordinates for storage)?  I didn't see anything
> >> in the documentation, so I was surprised to see some of the words in
> >> these posts ...
> >>
> >> Thanks
> >>
> >> On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote:
> >>
> >>> 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.
> >>>
> >>> Cheers!
> >>>
> >>> Mark
> >>>
> >>> 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 :-)
> >>>>
> >>>> Thanks,
> >>>> Scott
> >>>>
> >>>>
> >>>> 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>
> >>> Illuminae
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at portal.open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> > --  
> > ----------------------------------------------------------------------- 
> > -
> > Scott Cain, Ph. D.                                          
> > cain at cshl.org
> > GMOD Coordinator (http://www.gmod.org/)                      
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
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