From 6e9fd45573a9506640415057049e561302515736 Mon Sep 17 00:00:00 2001 From: cbk-guest Date: Tue, 2 Aug 2016 03:33:06 +0300 Subject: [PATCH] Autopkgtest added --- debian/README.source | 2 ++ debian/changelog | 7 ++++++ debian/ncbi-blast+.examples | 1 + debian/ncbi-blast+.tests/test.fa | 10 ++++++++ debian/ncbi-blast+.tests/testdatabase.fa | 29 ++++++++++++++++++++++++ debian/tests/control | 3 +++ debian/tests/run-unit-test | 24 ++++++++++++++++++++ 7 files changed, 76 insertions(+) create mode 100644 debian/ncbi-blast+.examples create mode 100644 debian/ncbi-blast+.tests/test.fa create mode 100644 debian/ncbi-blast+.tests/testdatabase.fa create mode 100644 debian/tests/control create mode 100644 debian/tests/run-unit-test diff --git a/debian/README.source b/debian/README.source index 6dde0846..85ca5993 100644 --- a/debian/README.source +++ b/debian/README.source @@ -4,4 +4,6 @@ blast+ for Debian Lintian raises hardening no fortify warnings that are false positives. +Test examples taken from http://www.ncbi.nlm.nih.gov/books/NBK52640/ +-- Canberk Koç Tue, 2 Aug 2016 03:30:33 +0300 diff --git a/debian/changelog b/debian/changelog index 6374d96a..c3be456c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +ncbi-blast+ (2.3.0-2) UNRELEASED; urgency=medium + + * Team upload. + * Autopkgtest added + + -- Canberk Koç Tue, 02 Aug 2016 03:32:09 +0300 + ncbi-blast+ (2.3.0-1) unstable; urgency=medium * New upstream version diff --git a/debian/ncbi-blast+.examples b/debian/ncbi-blast+.examples new file mode 100644 index 00000000..e5da4986 --- /dev/null +++ b/debian/ncbi-blast+.examples @@ -0,0 +1 @@ +debian/ncbi-blast+.tests/* diff --git a/debian/ncbi-blast+.tests/test.fa b/debian/ncbi-blast+.tests/test.fa new file mode 100644 index 00000000..6db78dd5 --- /dev/null +++ b/debian/ncbi-blast+.tests/test.fa @@ -0,0 +1,10 @@ +>gnl|MYDB|1 this is sequence 1 +GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG +TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA +GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT +GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG +GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT +TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG +CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT +TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT +CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA diff --git a/debian/ncbi-blast+.tests/testdatabase.fa b/debian/ncbi-blast+.tests/testdatabase.fa new file mode 100644 index 00000000..844ac1db --- /dev/null +++ b/debian/ncbi-blast+.tests/testdatabase.fa @@ -0,0 +1,29 @@ +>gnl1 +GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG +TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA +GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT +GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG +GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT +TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG +CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT +TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT +CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA +>gnl2 +GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG +TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA +GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT +GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG +GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT +TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG +CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT +TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT +CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA +>gnl3 +GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG +TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA +GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT +GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG +GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT +TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG +CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT +TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 00000000..d2aa55ae --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test new file mode 100644 index 00000000..7e48969b --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +pkg="ncbi-blast+" + +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP +find . -name "*.gz" -exec gunzip \{\} \; + +echo '---Creating Database--' +/usr/bin/makeblastdb -in testdatabase.fa -parse_seqids -dbtype nucl -out testdb +echo '---Searching Database for Hits---' +/usr/bin/blastn -query test.fa -db testdb -task blastn -dust no -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 2 +echo '---Search and Fetch An Entry From Database---' +/usr/bin/blastdbcmd -db testdb -entry gnl1 -out test_query.fa +cat test_query.fa + +echo "PASS" -- 2.30.2