#!/bin/bash
set -e

pkg="tigr-glimmer"

if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi

cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP
find . -name "*.gz" -exec gunzip \{\} \;

echo "g3-from-scratch"
echo "##################################"
tigr-glimmer long-orfs -n -t 1.15 example.fa run1.longorfs
tigr-glimmer extract -t example.fa run1.longorfs > run1.train
tigr-glimmer build-icm -r run1.icm < run1.train
tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run1.icm run1
echo "=================================="

# for making this test, need fasta file with coords
#echo "g3-from-training"
#echo "##################################"
#tigr-glimmer extract -t example.fa train.coords > run2.train
#tigr-glimmer build-icm -r run2.icm < run2.train
#tigr-glimmer upstream-coords.awk 25 0 train.coords | extract example.fa - > run2.upstream
##elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
##set startuse = ‘start-codon-distrib -3 example.fa train.coords‘
##tigr-glimmer glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse example.fa run2.icm run2

echo "g3-iterated"
echo "##################################"
tigr-glimmer long-orfs -n -t 1.15 example.fa run3.longorfs
tigr-glimmer extract -t example.fa run3.longorfs > run3.train
tigr-glimmer build-icm -r run3.icm < run3.train
tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run3.icm run3.run1
tail -n+2 run3.run1.predict > run3.coords
# for making full test, need elph (elph not in repo)
#upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
#elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
#set startuse = ‘start-codon-distrib -3 genom.seq run3.coords‘
#tigr-glimmer glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
echo "=================================="

echo "PASS"