#!/bin/sh
echo "run Glimmer3"
clear
echo "Genome is " $1
echo "Find non-overlapping orfs in  tmp.coord"
BINDIR="/usr/lib/tigr-glimmer"
rm -f tmp.coord
${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord
echo "Extract training sequences to tmp.train"
rm -f tmp.train
${BINDIR}/extract $1 tmp.coord >tmp.train
wc tmp.train
echo "Build interpolated context model in  tmp.model"
rm -f tmp.model
${BINDIR}/build-icm <tmp.train >tmp.model
echo "Predict genes with Glimmer3 with coordinates in  g3.coord"
rm -f g3.coord
# get-putative is ot contained in version 3.x any more
# ${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord
${BINDIR}/glimmer3 $1 tmp.model >g3.coord