[Bioperl-l] GlimmerM parser

[Jason Stajich]

For the annotation work I'm doing I'm generating a bunch of scripts and
a few modules.  Here's what I've just committed and some future stuff.
Feel free to chime in if you have other things yourself.


I've added a parser for the ab initio gene predictor GlimmerM in
Bio::Tools::Glimmer.  Tests are added to t/Genpred.t now.

It follows the Bio::Tools::AnalysisParser interface which support the
next_prediction call and returns a Bio::Tools::Prediction::Gene object in
the same way as Genscan.

I also have some scripts for building the training set file so you can run
Glimmer on other species.  There is also a similar script for building
custom splice sites file for Genewise which I'll commit soon.  Basically
it takes as input a GFF file which has exons annotated (typically from
Sim4/Exonerate alignments of cDNA to DNA) and a reference to the genomic
DNA db (typically just a flatfile which we index with Bio::DB::Flat).

Not sure where to put these - scripts/gene_prediction ?


-jason

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu