Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits:
2da3cb75 by Liubov Chuprikova at 2018-04-02T14:40:23+00:00
Autopkgtest. Added test for tbl2asn. Fixed typo
- - - - -
4 changed files:
- debian/tests/run-unit-test
- + debian/tests/test-data/Sc_16.fsa
- + debian/tests/test-data/Sc_16.sbt
- + debian/tests/test-data/Sc_16.tbl
Changes:
=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -9,7 +9,8 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/test-data/* .
-gunzip nc0305.aso.gz
+cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.ent} .
+gunzip *.gz
echo '---asn2all test---'
/usr/bin/asn2all -i nc0305.aso -b -f g -o nc0305.nuc -v nc0305.prt
@@ -25,7 +26,7 @@ echo '---asn2fsa test---'
[ -s nc0305.fna ]
[ -s nc0305.faa ]
-echo '---ans2gb test---'
+echo '---asn2gb test---'
/usr/bin/asn2gb -i nc0305.aso -b -a t -o nc0305.gbk
[ -s nc0305.gbk ]
@@ -47,6 +48,10 @@ echo '---asnval test---'
[ -f nc0305.val ]
[ ! -s nc0305.val ] # empty
+echo '---asntool test---'
+/usr/bin/asntool -m asnpub.all -v medline.ent -p asntool.output
+[ -s asntool.output ]
+
echo '---cleanasn test---'
/usr/bin/cleanasn -b -a t -D t -i nc0305.aso -o nc0305_cleaned.aso
[ -s nc0305_cleaned.aso ]
@@ -56,7 +61,7 @@ echo '---debruijn test---'
[ -s debruijn.output ]
echo '---gene2xml test---'
-/usr/bin/gene2xml -c -b -i dsRNA_viruses.ags.gz -o dsRNA_viruses.xgs
+/usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs
[ -s dsRNA_viruses.xgs ]
grep 'GI:' nc0305.gbk | head | sed 's/.*GI://' > GIs.txt
@@ -69,6 +74,10 @@ echo '---idfetch test---'
/usr/bin/idfetch -G GIs.txt -t 2 -o idfetch.aso
[ -s idfetch.aso ]
+echo '---tbl2asn test---'
+/usr/bin/tbl2asn -t Sc_16.sbt -i Sc_16.fsa
+[ -s Sc_16.sqn ]
+
echo '---trna2sap test---'
/usr/bin/trna2sap < trnascan-se_sample.output > trna2sap.output
[ -s trna2sap.output ]
@@ -76,9 +85,3 @@ echo '---trna2tbl test---'
/usr/bin/trna2tbl < trnascan-se_sample.output > trna2tbl.output
[ -s trna2tbl.output ]
-cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.ent} .
-gunzip asnpub.all.gz
-echo '---asntool test---'
-/usr/bin/asntool -m asnpub.all -v medline.ent -p asntool.output
-[ -s asntool.output ]
-
=====================================
debian/tests/test-data/Sc_16.fsa
=====================================
--- /dev/null
+++ b/debian/tests/test-data/Sc_16.fsa
@@ -0,0 +1,14 @@
+>Sc_16 [organism=Saccharomyces cerevisiae]
+tataggcgaatcgagtatattattttttctcaacatatgtat
+atgaacatgagaatatatttataggaatgtataaaattgtga
+cctctcctgctattttagttactgattttatgtatgtagggg
+gaataggggctgcctttcttaatgcagttttaattttttctt
+ttaattttttcttagtaaaattatttaaagtaaagattaatg
+gaataaccattgcgcttttttttacagtttttggtttttcat
+tttttggaaaaaatattttaaatattttacctttttatttag
+ggggtattttatatagtatctatacttcaacagatttttctg
+aacatatagttcctattgctttttcaagtgcattagcccctt
+ttgtaagcagtgttgctttttatggagaaatatcctatgaaa
+catcatatataaatgcaattttaattggtattttaattggtt
+ttatagtggttcctttgtctaaaagtctttatgactttcatg
+agggatatgatttatataatttaggttttacagcaggtt
=====================================
debian/tests/test-data/Sc_16.sbt
=====================================
--- /dev/null
+++ b/debian/tests/test-data/Sc_16.sbt
@@ -0,0 +1,43 @@
+Submit-block ::= {
+ contact {
+ contact {
+ name
+ name {
+ last "Darwin" ,
+ first "Charles" ,
+ initials "C.R." ,
+ suffix "" } ,
+ affil
+ std {
+ affil "Oxbridge University" ,
+ div "Evolutionary Biology Department" ,
+ city "Camford" ,
+ country "United Kingdom" ,
+ street "1859 Tennis Court Lane" ,
+ email "darwin at beagle.edu.uk" ,
+ phone "01 44 171-007-1212" ,
+ postal-code "OX1 2BH" } } } ,
+ cit {
+ authors {
+ names
+ std {
+ {
+ name
+ name {
+ last "Darwin" ,
+ first "Charles" ,
+ initials "C.R." } } } ,
+ affil
+ std {
+ affil "Oxbridge University" ,
+ div "Evolutionary Biology Department" ,
+ city "Camford" ,
+ country "United Kingdom" ,
+ street "1859 Tennis Court Lane" ,
+ postal-code "OX1 2BH" } } ,
+ date
+ std {
+ year 2003 ,
+ month 2 ,
+ day 28 } } ,
+ subtype new }
=====================================
debian/tests/test-data/Sc_16.tbl
=====================================
--- /dev/null
+++ b/debian/tests/test-data/Sc_16.tbl
@@ -0,0 +1,6 @@
+>Feature Sc_16 Table1
+69 543 gene
+ gene sde3p
+69 >543 CDS
+ product SDE3P
+ protein_id WS1030
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/2da3cb755eb96fb3b7a1ff3f73e41513fc64b62e
---
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/2da3cb755eb96fb3b7a1ff3f73e41513fc64b62e
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