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|
#!/bin/sh -f
# copied and enhanced from upstream
set -e
pkg=andi
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp test/test_fasta.cxx "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
g++ -O2 -Wall -o test_fasta test_fasta.cxx
RANDOM_SEED=1729
#--- only small changes below ---
andi --help > /dev/null || exit 1
SEED=${RANDOM_SEED:-0}
SEED2=0
SEED3=0
if test $SEED -ne 0; then
SEED=$((SEED + 1))
SEED2=$((SEED + 2))
SEED3=$((SEED + 3))
fi
# Simple join test
./test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta
./test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta
./test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta
head -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S0_join.fasta
tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta
rm p1_join.fasta p2_join.fasta p3_join.fasta;
RES=$(andi -m RAW -t 1 -j S0_join.fasta S1_join.fasta |
tail -n 1 |
awk '{print ($2 - 0.1)}' |
awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'
)
if test $RES -ne 1; then
echo "The last test computed a distance deviating more than three percent from its intended value."
echo "See S0_join.fasta and S1_join.fasta for the used sequences."
exit 1;
fi
SEED=${RANDOM_SEED:-0}
SEED2=0
if test $SEED -ne 0; then
SEED=$((SEED + 5))
SEED2=$((SEED + 6))
fi
#unbalanced number of contigs
./test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2_join.fasta
./test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3_join.fasta
head -qn 2 p3_join.fasta > S0_join.fasta
tail -qn 2 p2_join.fasta p3_join.fasta > S1_join.fasta
rm p2_join.fasta p3_join.fasta;
RES=$(andi -m RAW -t1 -j S0_join.fasta S1_join.fasta |
tail -n 1 |
awk '{print ($2 - 0.1)}' |
awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'
)
if test $RES -ne 1; then
echo "The last test computed a distance deviating more than three percent from its intended value."
echo "See S0_join.fasta and S1_join.fasta for the used sequences."
exit 1;
fi
SEED=${RANDOM_SEED:-0}
SEED2=0
SEED3=0
if test $SEED -ne 0; then
SEED=$((SEED + 11))
SEED2=$((SEED + 12))
SEED3=$((SEED + 13))
fi
#unbalanced number of contigs 2
./test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta
./test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta
./test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta
head -qn 2 p1_join.fasta p3_join.fasta > S0_join.fasta
tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta
rm p1_join.fasta p2_join.fasta p3_join.fasta;
RES=$(andi -mRAW -t 1 -j S0_join.fasta S1_join.fasta |
tail -n 1 |
awk '{print ($2 - 0.1)}' |
awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'
)
if test $RES -ne 1; then
echo "The last test computed a distance deviating more than three percent from its intended value."
echo "See S0_join.fasta and S1_join.fasta for the used sequences."
exit 1;
fi
rm S0_join.fasta S1_join.fasta
|
