Nilesh Patra pushed to branch master at Debian Med / bioawk
Commits: e3ca5c8e by Nilesh Patra at 2021-02-28T20:37:48+05:30 Change test dependency from swarm to seqkit-examples so as to test on all architectures - - - - - 7afac90b by Nilesh Patra at 2021-02-28T20:41:00+05:30 Update changelog - - - - - 3 changed files: - debian/changelog - debian/tests/control - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +bioawk (1.0-3) unstable; urgency=medium + + * Change test dependency from swarm to + seqkit-examples so as to test on all architectures + + -- Nilesh Patra <[email protected]> Sun, 28 Feb 2021 20:37:56 +0530 + bioawk (1.0-2) unstable; urgency=medium * Source-only-upload ===================================== debian/tests/control ===================================== @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: @, swarm, samtools-test +Depends: @, seqkit-examples, samtools-test Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -6,40 +6,41 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM fi -cp /usr/share/doc/swarm/test-data/input.fasta.gz $AUTOPKGTEST_TMP +cp /usr/share/doc/seqkit-examples/tests/SIRV_150601a.fasta.gz $AUTOPKGTEST_TMP cp /usr/share/samtools/test/ampliconclip/ac_test.bed $AUTOPKGTEST_TMP cp /usr/share/samtools/test/dat/view.001.sam $AUTOPKGTEST_TMP cd $AUTOPKGTEST_TMP gunzip -r * +mv SIRV_150601a.fasta input.fasta echo "Test 1 - Get length for sequences" -bioawk -c fastx '{ print $name, length($seq) }' input.fasta 1> test1 2> test1 +bioawk -c fastx '{ print $name, length($seq) }' input.fasta 1>test1 2>>test1 [ -s test1 ] || exit 1 echo "=================================" echo "PASS" echo "Test 2 - Get reverse compliment" -bioawk -c fastx '{ print ">"$name;print revcomp($seq) }' input.fasta 1>test2 2>test2 +bioawk -c fastx '{ print ">"$name;print revcomp($seq) }' input.fasta 1>test2 2>>test2 [ -s test2 ] || exit 1 echo "==================================" echo "PASS" echo "Test 3 - Convert FASTA to tabular form" -bioawk -t -c fastx '{ print $name, $seq }' input.fasta 1>test3 2>test3 +bioawk -t -c fastx '{ print $name, $seq }' input.fasta 1>test3 2>>test3 [ -s test3 ] || exit 1 echo "==================================" echo "PASS" echo "Test 4 - Print feature length" -bioawk -c bed '{ print $end - $start }' ac_test.bed 1>test4 2>test4 +bioawk -c bed '{ print $end - $start }' ac_test.bed 1>test4 2>>test4 [ "$(cat test4 | wc -l)" -gt 1 ] || exit 1 [ -s test4 ] || exit 1 echo "==================================" echo "PASS" echo "Test 5 - Extract mapped reads" -bioawk -c sam -H '!and($flag,4)' view.001.sam 1>test5 2>test5 +bioawk -c sam -H '!and($flag,4)' view.001.sam 1>test5 2>>test5 [ -s test5 ] || exit 1 echo "==================================" echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/compare/9309cf58153be8c547ea95eaffaeef2ba974cc94...7afac90bb68ed64888aa06ba6f436246003f74c9 -- View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/compare/9309cf58153be8c547ea95eaffaeef2ba974cc94...7afac90bb68ed64888aa06ba6f436246003f74c9 You're receiving this email because of your account on salsa.debian.org.
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