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#!/bin/bash
set -e
pkg="cd-hit"
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 "==== CD_HIT ===="
cd-hit -i example.fa -o out -c 1.00 -n 5 -M 0 -T 0
echo "==== CD_HIT-2D ===="
cd-hit-2d -i example.fa -i2 example.fa -o out -c 0.9 -n 5 -M 0 -T 0
echo "==== CD_HIT-EST ===="
cd-hit-est -i example.fa -o out -c 0.95 -n 10 -M 0 -T 0
echo "==== CD_HIT-EST-2D ===="
cd-hit-est-2d -i example.fa -i2 example.fa -o out -c 0.95 -n 10 -M 0 -T 0
echo "==== CD_HIT-454 ===="
cd-hit-454 -i example.fa -o out -c 0.95 -n 10 -M 0 -T 0
echo "==== CD_HIT-DIV ===="
cd-hit-div example.fa output 4
for i in `ls ./*output*` ; do
echo $i
cat $i
done
echo "PASS"
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