[Bioperl-l] writing GFF3

Chris Fields cjfields at illinois.edu
Wed Feb 10 08:27:35 EST 2010


Daniel,

I'm in the process of refactoring Bio::FeatureIO to remove Bio::SeqFeature::Annotated and work with Bio::DB::SeqFeature::Store, which may take a little time (I've started on the gff/gtf stuff already, just need to build the handler for the information and standardize a few things).  I would suggest going with Bio::DB::SeqFeature::Store's memory implementation if the features are few, or you could also try Bio::Tools::GFF.

chris

On Feb 10, 2010, at 1:44 AM, Daniel Renfro wrote:

> I'm working on a class to compare two Seq objects (tentatively called
> "SeqDiff" for now.) It works great, but as of now just spits out hashes of
> differences. Instead of printing these differences to the screen (which is
> fine for my test genome of 9 features) I would like to create some GFF3 that
> I can load into GBrowse. I could just print the 9 columns, but I'm sure
> there is something that could do this better/already. I found two packages
> in BioPerl, which one should I be using?
> 
> Bio::FeatureIO::gff
> Bio::Tools::gff
> 
> Also, I vaguely recall something being said about deprecating Bio::FeatureIO
> at the BioPerl meeting in San Diego (prior to the GMOD meeting.) -- or I
> could be mixing things up.
> 
> -Daniel Renfro
> 
> http://ecoliwiki.net/User:DanielRenfro
> Hu Lab Research Associate
> 979-862-4055
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