Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits: 71bca8b8 by Liubov Chuprikova at 2018-03-28T19:34:58+00:00 Autopkgtest. More tests, but will be more - - - - - 4 changed files: - debian/copyright - debian/source/include-binaries - debian/tests/run-unit-test - + debian/tests/test-data/dsRNA_viruses.ags.gz Changes: ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -13,12 +13,13 @@ Copyright: 1998-1999 Stephane Bortzmeyer <[email protected]> 2001-2017 Aaron M. Ucko <[email protected]> License: public_domain -Files: debian/tests/test-data/nc0305.aso.gz +Files: debian/tests/test-data Copyright: 1996-2018 NCBI License: public_domain Comment: GenBank Release 224.0 - To dowload the file use: + To dowload the files use: wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz + wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz License: public_domain The NCBI toolkit has been put into the public domain, completely unfettered: ===================================== debian/source/include-binaries ===================================== --- a/debian/source/include-binaries +++ b/debian/source/include-binaries @@ -1 +1,2 @@ debian/tests/test-data/nc0305.aso.gz +debian/tests/test-data/dsRNA_viruses.ags.gz ===================================== debian/tests/run-unit-test ===================================== --- a/debian/tests/run-unit-test +++ b/debian/tests/run-unit-test @@ -10,7 +10,7 @@ fi cd $AUTOPKGTEST_TMP -cp /usr/share/doc/${pkg}/test-data/nc0305.aso.gz . +cp -a /usr/share/doc/${pkg}/test-data/* . gunzip * echo '---asn2all test---' @@ -48,3 +48,26 @@ echo '---asnval test---' /usr/bin/asnval -i nc0305.aso -b -a t -o nc0305.val [ -f nc0305.val ] [ ! -s nc0305.val ] # empty + +echo '---cleanasn test---' +/usr/bin/cleanasn -b -a t -D t -i nc0305.aso -o nc0305_cleaned.aso +[ -s nc0305_cleaned.aso ] + +echo '---debruijn test---' +/usr/bin/debruijn -a ncbistdaa -n 4 > debruijn.output +[ -s debruijn.output ] + +echo '---gene2xml test---' +/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 +# insdseqget and idfetch testing requires internet connection. Comment lines below +# to skip the testing. +echo '---insdseqget test---' +/usr/bin/insdseqget -n -i GIs.txt > insdset.xml +[ -s insdset.xml ] +echo '---idfetch test---' +/usr/bin/idfetch -G GIs.txt -t 2 -o idfetch.aso +[ -s idfetch.aso ] + ===================================== debian/tests/test-data/dsRNA_viruses.ags.gz ===================================== Binary files /dev/null and b/debian/tests/test-data/dsRNA_viruses.ags.gz differ View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb --- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
