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#!/bin/bash
set -e
pkg=tnseq-transit
CUR_DIR=`pwd`
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 ${CUR_DIR}/src/pytransit/* -a "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip -r *
echo "Test 1"
transit gumbel data/cholesterol_H37Rv_rep1.wig,data/cholesterol_H37Rv_rep2.wig genomes/H37Rv.prot_table test1
[ -s test1 ] || exit 1
echo "PASS"
echo "Test 2"
transit tn5gaps data/cholesterol_H37Rv_rep1.wig,data/cholesterol_H37Rv_rep2.wig genomes/H37Rv.prot_table test2 -m 2 -r Sum -iN 5 -iC 5
[ -s test2 ] || exit 1
echo "PASS"
echo "Test 3"
transit normalize data/glycerol_H37Rv_rep1.wig data/glycerol_H37Rv_rep2.wig -n TTR
echo "PASS"
echo "Test 4"
transit tnseq_stats -c data/cholesterol_glycerol_combined.dat
echo "PASS"
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