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 ?