Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits: 6576aed1 by Liubov Chuprikova at 2018-04-08T23:15:17+00:00 Autopkgtest: improved a couple of tests by checking its output content - - - - - 1 changed file: - debian/tests/run-unit-test Changes: ===================================== debian/tests/run-unit-test ===================================== --- a/debian/tests/run-unit-test +++ b/debian/tests/run-unit-test @@ -14,44 +14,70 @@ cp /usr/share/ncbi/data/autofix.prt . cp /usr/share/ncbi/data/UniVec.* . gunzip *.gz -echo '---asn2all test---' -/usr/bin/asn2all -i nc0225.aso -b -f g -o nc0225.nuc -v nc0225.prt -[ -s nc0225.nuc ] -[ -s nc0225.prt ] - +################################################################## echo '---asn2asn test---' +################################################################## /usr/bin/asn2asn -i nc0225.aso -b -o nc0225.text +/usr/bin/asn2asn -i nc0225.text -s -o nc0225_new.aso [ -s nc0225.text ] +[ -s nc0225_new.aso ] +diff nc0225.aso nc0225_new.aso +rm nc0225.aso nc0225_new.aso +################################################################## +echo '---asn2all test---' +################################################################## +/usr/bin/asn2all -i nc0225.text -f g -o nc0225.nuc -v nc0225.prt +[ -s nc0225.nuc ] +genes_dna="$(grep -c " mol dna ," nc0225.text)" +genes_rna="$(grep -c " mol rna ," nc0225.text)" +genes=$(expr $genes_dna + $genes_rna) +nuc="$(grep -c "^LOCUS " nc0225.nuc)" +[ $genes -eq $nuc ] +[ -s nc0225.prt ] +proteins="$(grep -c " mol aa ," nc0225.text)" +prt="$(grep -c "^LOCUS " nc0225.prt)" +[ $proteins -eq $prt ] + +################################################################## echo '---asn2fsa test---' -/usr/bin/asn2fsa -i nc0225.aso -b -a t -o nc0225.fna -v nc0225.faa +################################################################## +/usr/bin/asn2fsa -i nc0225.text -a t -o nc0225.fna -v nc0225.faa [ -s nc0225.fna ] +fna="$(grep -c "^>" nc0225.fna)" +[ $genes -eq $fna ] [ -s nc0225.faa ] +faa="$(grep -c "^>" nc0225.faa)" +[ $proteins -eq $faa ] +################################################################## echo '---asn2gb test---' -/usr/bin/asn2gb -i nc0225.aso -b -a t -o nc0225.gbk +################################################################## +/usr/bin/asn2gb -i nc0225.text -a t -o nc0225.gbk [ -s nc0225.gbk ] +gbk="$(grep -c "^LOCUS " nc0225.gbk)" +[ $genes -eq $gbk ] + echo '---asn2idx test---' -/usr/bin/asn2idx -b -p . < nc0225.aso +/usr/bin/asn2idx -p . -x .text < nc0225.text [ -s nc0225.idx ] [ -s master.idx ] echo '---asn2xml test---' -/usr/bin/asn2xml -i nc0225.aso -o nc0225.xml +/usr/bin/asn2xml -i nc0225.text -b F -o nc0225.xml [ -s nc0225.xml ] echo '---asndisc test---' -/usr/bin/asndisc -i nc0225.aso -b -a t -o nc0225.disc +/usr/bin/asndisc -i nc0225.text -a t -o nc0225.disc [ -s nc0225.disc ] echo '---asnval test---' -/usr/bin/asnval -i nc0225.aso -b -a t -o nc0225.val -[ -f nc0225.val ] -[ ! -s nc0225.val ] # empty +/usr/bin/asnval -i nc0225.text -a t -o nc0225.val -Q 2 +[ -s nc0225.val ] echo '---asnmacro test---' -/usr/bin/asnmacro -i nc0225.aso -b -m autofix.prt -o asnmacro.output +/usr/bin/asnmacro -i nc0225.text -m autofix.prt -o asnmacro.output [ -s asnmacro.output ] echo '---asntool test---' @@ -59,8 +85,8 @@ echo '---asntool test---' [ -s asntool.output ] echo '---cleanasn test---' -/usr/bin/cleanasn -b -a t -D t -i nc0225.aso -o nc0225_cleaned.aso -[ -s nc0225_cleaned.aso ] +/usr/bin/cleanasn -a t -D t -i nc0225.text -o nc0225_cleaned.text +[ -s nc0225_cleaned.text ] echo '---debruijn test---' /usr/bin/debruijn -a ncbistdaa -n 4 > debruijn.output @@ -70,9 +96,9 @@ echo '---gene2xml test---' /usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs [ -s dsRNA_viruses.xgs ] -grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt # _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 echo '---insdseqget test---' /usr/bin/insdseqget -n -i GIs.txt > insdset.xml [ -s insdset.xml ] View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/6576aed1e8963efbf350b53b881fa5f6413887d3 --- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/6576aed1e8963efbf350b53b881fa5f6413887d3 You're receiving this email because of your account on salsa.debian.org.
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