Commit 55d6cb5e authored by Liubov Chuprikova's avatar Liubov Chuprikova
Browse files

Autopkgtest: Added a few more tests

parent fac5500e

debian/ncbi-tools-bin.docs

+1 −1
Original line number Diff line number Diff line
@@ -5,4 +5,4 @@ debian/README.test 
debian/tests/run-unit-test

debian/tests/test-data

asn/asnpub.all

demo/medline.ent
 
demo/medline.prt

debian/tests/run-unit-test

+36 −6
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then 
fi

cd $AUTOPKGTEST_TMP

cp -a /usr/share/doc/${pkg}/test-data/* .

cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.ent} .

cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.prt.gz} .

cp /usr/share/ncbi/data/autofix.prt .

cp /usr/share/ncbi/data/UniVec.* .

gunzip *.gz
@@ -25,8 +25,8 @@ check_GI() 
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 ]

/usr/bin/asn2asn -i nc0225.text -s -o nc0225_new.aso

[ -s nc0225_new.aso ]

diff nc0225.aso nc0225_new.aso

rm nc0225.aso nc0225_new.aso
@@ -112,10 +112,9 @@ end_in="$(grep -c "^${last_id}" dsRNA_viruses.gene_info)" 
end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"

[ $end_in -eq $end_out ]





if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then

grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt



if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then

	##################################################################

	echo '---insdseqget test---'

	##################################################################
@@ -128,6 +127,13 @@ if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then 
	/usr/bin/idfetch -G GIs.txt -o idfetch.text

	[ -s idfetch.text ]

	check_GI idfetch.text GIs.txt



	##################################################################

	echo '---makeset test---'

	##################################################################

	echo 'idfetch.text' > files

	/usr/bin/makeset -i files -o makeset.aso

	[ -s makeset.aso ]

fi
@@ -154,17 +160,41 @@ echo '---asnmacro test---' 
[ -s asnmacro.output ]



echo '---asntool test---'

/usr/bin/asntool -m asnpub.all -v medline.ent -p asntool.output

[ -s asntool.output ]

/usr/bin/asntool -m asnpub.all -v medline.prt -e medline.val

[ -s medline.val ]



echo '---indexpub test---'

/usr/bin/indexpub -i medline.val

[ -s medline.idx ]



echo '---getpub test---'

/usr/bin/getpub -i medline.val -o getpub.output

[ -s getpub.output ]



echo '---getmesh test---'

/usr/bin/getmesh -i getpub.output -o getmesh.output

[ -s getmesh.output ]



echo '---debruijn test---'

/usr/bin/debruijn -a ncbistdaa -n 4 > debruijn.output

[ -s debruijn.output ]



echo '---gil2bin test---'

/usr/bin/gil2bin -i GIs.txt -o GIs.bin

[ -s GIs.bin ]



echo '---tbl2asn test---'

/usr/bin/tbl2asn -t Sc_16.sbt -i Sc_16.fsa

[ -s Sc_16.sqn ]



echo '---checksub test---'

/usr/bin/checksub -i Sc_16.sqn -o checksub.sqn

diff Sc_16.sqn checksub.sqn



echo '---subfuse test---'

/usr/bin/subfuse -p ./ -o subfuse.output

[ -s subfuse.output ]



echo '---trna2sap test---'

/usr/bin/trna2sap < trnascan-se_sample.output > trna2sap.output

[ -s trna2sap.output ]