Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits: 474ec7bc by Liubov Chuprikova at 2018-04-12T12:32:51+00:00 Autopkgtest: improved one test, amended README.test - - - - - 2 changed files: - debian/README.test - debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== --- a/debian/README.test +++ b/debian/README.test @@ -3,6 +3,6 @@ _______________________________________ This package can be tested by execution - sh run-unit-test + bash run-unit-test in order to confirm its integrity. ===================================== debian/tests/run-unit-test ===================================== --- a/debian/tests/run-unit-test +++ b/debian/tests/run-unit-test @@ -14,6 +14,13 @@ cp /usr/share/ncbi/data/autofix.prt . cp /usr/share/ncbi/data/UniVec.* . gunzip *.gz +check_GI() +{ + while read GI; do + grep -q $GI $1 + done < $2 +} + ################################################################## echo '---asn2asn test---' ################################################################## @@ -59,6 +66,15 @@ gbk="$(grep -c "^LOCUS " nc0225.gbk)" [ $genes -eq $gbk ] ################################################################## +echo '---asn2idx test---' +################################################################## +/usr/bin/asn2idx -p . -x .text < nc0225.text +[ -s nc0225.idx ] +[ -s master.idx ] +awk 'NR == 1 || NR % 50 == 0 {print $1}' nc0225.idx | sed 's/\.1//' > indexed_GIs +check_GI nc0225.text indexed_GIs + +################################################################## echo '---asn2xml test---' ################################################################## /usr/bin/asn2xml -i nc0225.text -b F -o nc0225.xml @@ -100,12 +116,6 @@ end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)" # _insdseqget_ and _idfetch_ testing requires internet connection. # Comment the lines below to skip the testing. grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt -check_GI() -{ - while read GI; do - grep -q $GI $1 - done < $2 -} ################################################################## echo '---insdseqget test---' ################################################################## @@ -130,11 +140,6 @@ last_out="$(grep ">" vecscreen.output | tail -1 | sed 's/>Vector //' | sed 's/ . [ $last_in==$last_out ] -echo '---asn2idx test---' -/usr/bin/asn2idx -p . -x .text < nc0225.text -[ -s nc0225.idx ] -[ -s master.idx ] - echo '---asndisc test---' /usr/bin/asndisc -i nc0225.text -a t -o nc0225.disc [ -s nc0225.disc ] View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46 --- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46 You're receiving this email because of your account on salsa.debian.org.
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