echo "run Glimmer2"
clear
echo "Genome is " $1
echo "Find non-overlapping orfs in  tmp.coord"
rm -f tmp.coord
long-orfs $1 | get-putative >tmp.coord
echo "Extract training sequences to  tmp.train"
rm -f tmp.train
extract $1 tmp.coord >tmp.train
wc tmp.train
echo "Build interpolated context model in  tmp.model"
rm -f tmp.model
build-icm <tmp.train >tmp.model
echo "Predict genes with Glimmer2 with coordinates in  g2.coord"
rm -f g2.coord
glimmer2 $1 tmp.model | get-putative >g2.coord
