[Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO

[Allen Day]

On Sun, 17 Oct 2004, Steffen Grossmann wrote:

> Ok, ok, if you really want to convince me that Bio::FeatureIO::gff is 
> the technology of the future... (although I would also like to hear 
> Chris Mungall's opinion on this point...)

I'd like to hear Chris weigh in as well.

> So let's get back to the technicalities.
> 
> There is something which prevents the use of 
> Bio::SeqFeature::Tools::IDHandler with Bio::FeatureIO::gff, namely the 
> extensive use of the tag/value annotation system in the former. On one 
> hand, this comes from repeated calls of Bio::SeqFeatureI's 'primary_id' 
> method, on the other hand there are calls of 'get_tagset_values'.

We can map Bio::SeqFeature::Annotated::primary_id to something reasonable
in the AnnotationCollection, but my guess is that avoiding the tagset will
be more difficult.

I'd prefer not to add SeqFeatureI compliance as far as tagset methods go
-- one of the main reasons I added SeqFeature::Annotated was to get rid of
this "feature".  I haven't looked at the AnnotationAdaptor you mention 
below, but it sounds like a reasonable approach.

Regarding your earlier mail about returning unflattened features, we can 
do this pretty easily by implementing GFF3 '###' tag handling.  I don't 
remember if I mentioned this before.

-Allen

> I am not completely sure, but I think that compliance of 
> Bio::SeqFeature::Tools::IDHandler with both concepts can be achieved by 
> two changes:
> 
> 1) Bio::SeqFeatureI::primary_id and Bio::SeqFeature::Annotated have to 
> be made compatible. Just create a Bio::SeqFeature::Annotated object and 
> try to call 'primary_id' on it to see that it isn't at the moment. In 
> principle this can be done by storing the ID in the 
> AnnotationCollectionI object when the tag/value system is not present. 
> The problem is that the tag/value system is present in 
> Bio::SeqFeature::Annotated (it has to be, because it implements 
> Bio::SeqFeatureI), but it is not functional. Any suggestions?
> 
> 2) Bio::SeqFeature::Tools::IDHandler can be made compatible with both 
> annotation systems by using the Bio::SeqFeature::AnnotationAdaptor 
> module. This should  not cause any problems...
> 
> Steffen
> 
>  
> 
> Allen Day wrote:
> 
> >On Thu, 14 Oct 2004, Steffen Grossmann wrote:
> >
> >  
> >
> >>Dear Allen,
> >>
> >>I meanwhile understood that Bio::Tools::GFF in connection with 
> >>Bio::SeqFeature::Tools::IDHandler is doing a lot of the stuff I'd like 
> >>to have. Somehow, Bio::FeatureIO::gff seems to be a parallel development 
> >>to the first alternative. I don't know in how far there are plans to 
> >>    
> >>
> >
> >I don't see from a quick look at the source how Bio::Tools::GFF is related
> >to Bio::SeqFeature::Tools::IDHandler.  There's nothing preventing use of
> >the IDHandler in Bio::FeatureIO::gff, in fact it sounds like what you've
> >proposed to add so part of your work is already done.
> >
> >  
> >
> >>bring the two approaches together, but at the moment that seems to be 
> >>more complicated than just bringing one approach to an acceptable state. 
> >>Since the Bio::Tools::GFF approach seems to be ahead, I will focus on it 
> >>at the moment.
> >>    
> >>
> >
> >I would advise against adding more features into Bio::Tools::GFF.  I can't
> >speak for all others, but my future development will not use it, and I'm
> >in the process of converting code which does use it to depend on
> >Bio::FeatureIO::gff.
> >
> >-Allen
> >
> >  
> >
> 
> 
>