[Bioperl-l] writing GFF3

Scott Cain scott at scottcain.net
Wed Feb 10 10:16:07 EST 2010


Hi Daniel,

What I would do depends on how complicated your features are.  If
there are not parent child relationships, it would probably be easiest
to just print the GFF yourself rather than going through a module.
The beauty of GFF3 is that it is pretty easy to write (at least for
the simple stuff).  If it is more complicated, you could look at using
one of the BioPerl modules.

Scott

On Wed, Feb 10, 2010 at 2:44 AM, Daniel Renfro <bluecurio at gmail.com> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


More information about the Bioperl-l mailing list