[med-svn] [ncbi-blast+] 01/01: Autopkgtest added

[Canberk Koç]

This is an automated email from the git hooks/post-receive script.

cbk-guest pushed a commit to branch master
in repository ncbi-blast+.

commit 6e9fd45573a9506640415057049e561302515736
Author: cbk-guest <cbk-guests at scm.alioth.debian.org>
Date:   Tue Aug 2 03:33:06 2016 +0300

    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(+)

diff --git a/debian/README.source b/debian/README.source
index 6dde084..85ca599 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 <canberkkoc at gmail.com> Tue, 2 Aug 2016 03:30:33 +0300
diff --git a/debian/changelog b/debian/changelog
index 6374d96..c3be456 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 <canberkkoc at gmail.com>  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 0000000..e5da498
--- /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 0000000..6db78dd
--- /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 0000000..844ac1d
--- /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 0000000..d2aa55a
--- /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 0000000..7e48969
--- /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"

-- 
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