#!/bin/sh
echo "run Glimmer3"
clear
echo "Genome is " $1
echo "Find non-overlapping orfs in  tmp.coord"
rm -f tmp.coord
tigr-long-orfs $1 | tigr-get-putative >tmp.coord
echo "Extract training sequences to  tmp.train"
rm -f tmp.train
tigr-extract $1 tmp.coord >tmp.train
wc tmp.train
echo "Build interpolated context model in  tmp.model"
rm -f tmp.model
tigr-build-icm <tmp.train >tmp.model
echo "Predict genes with Glimmer3 with coordinates in  g3.coord"
rm -f g3.coord
tigr-glimmer3 $1 tmp.model | tigr-get-putative >g3.coord