[Bioperl-l] writing GFF3

Daniel Renfro bluecurio at gmail.com
Wed Feb 10 02:44:59 EST 2010


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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