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#!/usr/bin/env bash
function unpack_test_data() {
t=tests.tar.gz
if [ ! -f $t ]; then
echo "Error: file $t not found!"
exit 1
fi
echo "..unpacking test data.."
echo
tar -xzf $t
if [ ! -f tests/human-chr19_P.gff ]; then
echo "Error: invalid test data archive?"
exit 1
fi
/bin/rm -f tests.tar.gz
#cp tests_exp_out/*.gtf tests/ 2>/dev/null
}
#if [ ! -f tests/human-chr19_P.gff ]; then
if [ -f tests.tar.gz ]; then
#extract the tarball and rename the directory
echo "..Using existing ./tests.tar.gz"
unpack_test_data
else
echo "..Downloading test data.."
#use curl to fetch the tarball from a specific github release or branch
curl -ksLO https://github.com/gpertea/stringtie/raw/test_data/tests.tar.gz
unpack_test_data
fi
# fi
cd tests
# array element format:
#
arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads" \
"mix_short mix_long" "mix_short mix_long")
arrparms=("" "" "-L" "-L -G human-chr19_P.gff" "--mix" "--mix -G mix_guides.gff")
arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided" \
"mix_reads" "mix_reads_guided")
arrmsg=("Short reads" "Short reads and super-reads" "Long reads" \
"Long reads with annotation guides" "Mixed reads" "Mixed reads with annotation guides")
for i in ${!arrmsg[@]}; do
fout="${arrout[$i]}.out.gtf"
/bin/rm -f $fout
fcmp="${arrout[$i]}.out_expected.gtf"
if [ ! -f $fcmp ]; then
echo "Error: file $fcmp does not exist! Re-download test data."
exit 1
fi
n=$i
((n++))
echo "Test ${n}: ${arrmsg[$i]}"
fin=${arrins[$i]}.bam
if [[ ${arrins[$i]} =~ ^mix ]]; then
ins=( ${arrins[$i]} )
fin="${ins[0]}.bam ${ins[1]}.bam"
fi
../stringtie ${arrparms[$i]} -o $fout $fin
if [ ! -f $fout ]; then
echo "Error: file $fout not created! Failed running stringtie on $fin"
exit 1
fi
if diff -q -I '^#' $fout $fcmp &>/dev/null; then
echo " OK."
else
echo "Error: test failed, output $fout different than expected ($fcmp)!"
#exit 1
fi
done
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