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#! /bin/sh
set -e
pkg=pyfastx
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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cd "${AUTOPKGTEST_TMP}"
cp -a /usr/share/doc/${pkg}/examples/* .
# Keep some compressed files for later, as they are expected to remain so.
cp test.fa.gz test.fa.gz.keep
cp test.fq.gz test.fq.gz.keep
gunzip *.gz
mv test.fa.gz.keep test.fa.gz
mv test.fq.gz.keep test.fq.gz
# Note: reference results were obtained by running the command manually during
# the initial packaging. They may need to be adjusted if the command output
# were to change for, say, cosmetic reasons.
echo '$ pyfastx --help'
pyfastx --help
readonly PYFASTX_COMMANDS="$(
pyfastx --help \
| sed -n 's/^ \([^ ]\+\) .*$/\1/p' \
| xargs
)"
echo "\$ # Found pyfastx commands: '$PYFASTX_COMMANDS'"
for PYFASTX_COMMAND in ${PYFASTX_COMMANDS}
do
echo "\$ pyfastx $PYFASTX_COMMAND --help"
pyfastx "$PYFASTX_COMMAND" --help
done
echo '$ pyfastx --version'
pyfastx --version
# Try indexing everything.
for FASTX in *.fa *.fq *.fa.gz *.fq.gz
do
echo '$ pyfastx index '"$FASTX"
pyfastx index "$FASTX"
test -s "${FASTX}.fxi"
done
echo '$ pyfastx stat protein.fa'
pyfastx stat protein.fa
# Compare output, if that makes sense.
pyfastx stat protein.fa > result
cat > expected << END
fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50
protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4
END
diff -Naur expected result
echo '$ pyfastx split -n 2 protein.fa'
pyfastx split -n 2 protein.fa
test -s protein.1.fa
test -s protein.2.fa
echo '$ pyfastx fq2fa test.fq -o test.fa'
pyfastx fq2fa test.fq -o test.fa
test -s test.fa
# Get the four first characters of the first region.
echo '$ pyfastx subseq protein.fa UPI0000000011:1-4'
pyfastx subseq protein.fa UPI0000000011:1-4
# Compare results if that makes sense.
pyfastx subseq protein.fa UPI0000000011:1-4 -o result
cat > expected << END
>UPI0000000011:1-4
MVDA
END
diff -Naur expected result
# Sampling is random, don't try to check output too finely.
echo '$ pyfastx sample -n 1 test.fq.gz -o sample.fq'
pyfastx sample -n 1 test.fq.gz -o sample.fq
test -s sample.fq
# Get the first region.
echo '$ pyfastx extract protein.fa UPI0000000011'
pyfastx extract protein.fa UPI0000000011
# Compare results, if that makes sense.
pyfastx extract protein.fa UPI0000000011 -o result
cat > expected << END
>UPI0000000011 status=active
MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY
IPGTIILYATYVKSLLMKS
END
diff -Naur expected result
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