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#!/bin/bash
set -e
pkg="probcons"
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
/usr/bin/probcons example.fa > output1
/usr/bin/probcons -clustalw example.fa > output2.aln
/usr/bin/probcons -c 1 example.fa > output3.mfa
/usr/bin/probcons --consistency 1 example.fa > output4.mfa
/usr/bin/probcons -ir 1000 example.fa > output5.mfa
/usr/bin/probcons --iterative-refinement 1000 example.fa > output6.mfa
/usr/bin/probcons -pre 1 example.fa > output7.mfa
/usr/bin/probcons --pre-training 1 example.fa > output8.mfa
/usr/bin/probcons -pairs example.fa > output9.mfa
/usr/bin/probcons -viterbi example.fa > output10.mfa
/usr/bin/probcons -v example.fa > output11.mfa
/usr/bin/probcons --verbose example.fa > output12.mfa
echo "PASS"
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