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

Steffen Grossmann grossman at molgen.mpg.de
Sun Oct 17 12:05:19 EDT 2004

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...)

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'.

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...



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

%            Steffen Grossmann                %
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