Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6

Commits:
55d6cb5e by Liubov Chuprikova at 2018-04-16T21:33:09+00:00
Autopkgtest: Added a few more tests

- - - - -


2 changed files:

- debian/ncbi-tools-bin.docs
- debian/tests/run-unit-test


Changes:

=====================================
debian/ncbi-tools-bin.docs
=====================================
--- a/debian/ncbi-tools-bin.docs
+++ b/debian/ncbi-tools-bin.docs
@@ -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
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -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 ]
 
+grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
 
 if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then
-       grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
-
        ##################################################################
        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 ]



View it on GitLab: 
https://salsa.debian.org/med-team/ncbi-tools6/commit/55d6cb5ed278959872de91a8053c2cd71b5d6e1e

---
View it on GitLab: 
https://salsa.debian.org/med-team/ncbi-tools6/commit/55d6cb5ed278959872de91a8053c2cd71b5d6e1e
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