[med-svn] r18562 - in trunk/packages/plink/trunk/debian: . output_tests tests

[Dylan Aïssi]

Author: bob.dybian-guest
Date: 2015-01-10 22:48:16 +0000 (Sat, 10 Jan 2015)
New Revision: 18562

Added:
   trunk/packages/plink/trunk/debian/output_tests/
   trunk/packages/plink/trunk/debian/output_tests/README
   trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc
   trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq
   trunk/packages/plink/trunk/debian/tests/
   trunk/packages/plink/trunk/debian/tests/control
   trunk/packages/plink/trunk/debian/tests/run-sample-analysis
Modified:
   trunk/packages/plink/trunk/debian/changelog
   trunk/packages/plink/trunk/debian/control
   trunk/packages/plink/trunk/debian/examples
Log:
Add autopkgtest

Modified: trunk/packages/plink/trunk/debian/changelog
===================================================================
--- trunk/packages/plink/trunk/debian/changelog	2015-01-10 22:36:51 UTC (rev 18561)
+++ trunk/packages/plink/trunk/debian/changelog	2015-01-10 22:48:16 UTC (rev 18562)
@@ -7,6 +7,7 @@
 
   [ Dylan Aïssi ]
   * debian/control: Bump Policy to 3.9.6 (no changes needed)
+  * Add autopkgtest
 
  -- Dylan Aïssi <bob.dybian at gmail.com>  Sat, 10 Jan 2015 23:30:46 +0100
 

Modified: trunk/packages/plink/trunk/debian/control
===================================================================
--- trunk/packages/plink/trunk/debian/control	2015-01-10 22:36:51 UTC (rev 18561)
+++ trunk/packages/plink/trunk/debian/control	2015-01-10 22:48:16 UTC (rev 18562)
@@ -7,6 +7,7 @@
  Charles Plessy <plessy at debian.org>,
  Dylan Aïssi <bob.dybian at gmail.com>
 Build-Depends: debhelper (>= 9), zlib1g-dev
+Testsuite: autopkgtest
 Standards-Version: 3.9.6
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plink/trunk/

Modified: trunk/packages/plink/trunk/debian/examples
===================================================================
--- trunk/packages/plink/trunk/debian/examples	2015-01-10 22:36:51 UTC (rev 18561)
+++ trunk/packages/plink/trunk/debian/examples	2015-01-10 22:48:16 UTC (rev 18562)
@@ -1,2 +1,6 @@
+# Upstream samples files
 test.ped
 test.map
+
+# Expected outputs for autopkgtest
+debian/output_tests

Added: trunk/packages/plink/trunk/debian/output_tests/README
===================================================================
--- trunk/packages/plink/trunk/debian/output_tests/README	                        (rev 0)
+++ trunk/packages/plink/trunk/debian/output_tests/README	2015-01-10 22:48:16 UTC (rev 18562)
@@ -0,0 +1,11 @@
+# Output files (i.e. expected.plink.assoc and expected.plink.frq) were generated following:
+
+wget http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-x86_64.zip
+unzip plink-1.07-x86_64.zip
+cd plink-1.07-x86_64
+
+./plink --noweb --file test --freq
+mv plink.freq expected.plink.freq
+
+./plink --noweb --file test --assoc
+mv plink.assoc expected.plink.assoc

Added: trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc
===================================================================
--- trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc	                        (rev 0)
+++ trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc	2015-01-10 22:48:16 UTC (rev 18562)
@@ -0,0 +1,3 @@
+ CHR  SNP         BP   A1      F_A      F_U   A2        CHISQ            P           OR 
+   1 snp1          1    A   0.1667      0.5    C          1.5       0.2207          0.2 
+   1 snp2          2    G   0.1667   0.6667    T        3.086      0.07898          0.1 

Added: trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq
===================================================================
--- trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq	                        (rev 0)
+++ trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq	2015-01-10 22:48:16 UTC (rev 18562)
@@ -0,0 +1,3 @@
+ CHR  SNP   A1   A2          MAF  NCHROBS
+   1 snp1    A    C       0.3333       12
+   1 snp2    G    T       0.4167       12

Added: trunk/packages/plink/trunk/debian/tests/control
===================================================================
--- trunk/packages/plink/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/plink/trunk/debian/tests/control	2015-01-10 22:48:16 UTC (rev 18562)
@@ -0,0 +1,2 @@
+Tests: run-sample-analysis
+Depends: @

Added: trunk/packages/plink/trunk/debian/tests/run-sample-analysis
===================================================================
--- trunk/packages/plink/trunk/debian/tests/run-sample-analysis	                        (rev 0)
+++ trunk/packages/plink/trunk/debian/tests/run-sample-analysis	2015-01-10 22:48:16 UTC (rev 18562)
@@ -0,0 +1,23 @@
+#!/bin/sh -e
+# http://dep.debian.net/deps/dep8/
+# Autopkgtest: Test if plink run analysis correctly
+# Author: Dylan Aïssi <bob.dybian at gmail.com>
+# Last-Update: 2015-01-10
+
+pkg=plink
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/output_tests/* $ADTTMP
+
+# Allele frequencies
+plink --noweb --file test --freq
+diff plink.frq expected.plink.frq
+
+# Case/control or QTL association
+plink --noweb --file test --assoc
+diff plink.assoc expected.plink.assoc
+
+rm -f $ADTTMP/*
+