[Bioperl-l] GFF3 - Bioperl - SO

[Aaron J. Mackey]

Bio::Feature::IO::GFF is maybe what you want; available now in CVS, and 
soon in BioPerl 1.5

-Aaron

On Oct 11, 2004, at 9:20 AM, Steffen Grossmann wrote:

> Dear all,
>
> I fancy very much the approach taken by SO(FA) 
> (http://song.sourceforge.net/) to standardize the vocabulary used for 
> sequence annotation. Also, the GFF3 format is a nice way to represent 
> SO-compatible annotations and it would be a great thing to have this 
> all working seamlessly with bioperl.
>
> A first step towards such a seamless integration into bioperl would be 
> a parser which is able to read/write hierarchically nested feature 
> collections from/to GFF3 files. Such a parser should make use of the 
> GFF3 specific 'ID' and 'Parent' tags.
>
> Of course, I know about the 'Bio::Tools::GFF' and 
> 'Bio::SeqFeature::Tools' modules, where some related stuff can be 
> found. The problem is that the 'Bio::Tools::GFF' module doesn't 
> respect the 'Parent' and 'ID' tag structure and grouping in the 
> 'Unflattener' approach is also done conceptually different.
>
> Does anybody know about whether there is someone working on such a 
> project? Or, if there is no such project, is someone interested in 
> joining to start it?
>
> Thanks in advance for any response!
>
> Steffen
>
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--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697