[Genabel-commits] r999 - pkg/ProbABEL/tests

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2012-11-05 00:19:39 +0100 (Mon, 05 Nov 2012)
New Revision: 999

Modified:
   pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
Log:
In ProbABEL tests: 
- Rewrote the chec_probabel.pl_chunk.sh script to get rid of Bashisms and make it POSIX sh compatible.
- Fixed major bug introduced in previous commit of this file. The introduction of the functions lead to not all cases being tested. Furthermore, a negative diff wasn't caught and only the last diff was used to check the exit status )and thus lead to an OK or fail of the whole check. Now the script exits as soon as a diff fails. 


Modified: pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
===================================================================
--- pkg/ProbABEL/tests/check_probabel.pl_chunk.sh	2012-11-04 13:42:07 UTC (rev 998)
+++ pkg/ProbABEL/tests/check_probabel.pl_chunk.sh	2012-11-04 23:19:39 UTC (rev 999)
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 # L.C. Karssen
 # This script is used to test whether probabel.pl works correctly when
 # input is cut up in chunks
@@ -41,9 +41,9 @@
 
 
 # ---------- function definitions ----------
-function prepare_input
+prepare_input ()
 {
-    if [ "$1" == "nochunk" ]; then
+    if [ "$1" = "nochunk" ]; then
 	# ------------------ No chunks test -------------------
 	# Split the dose, prob and info files up into two chromosomes
 	# with some  chunks
@@ -62,7 +62,7 @@
 	sed -n '4,6p' $mapfile >> chr2.map
 
 	WithOrWithout="without"
-    elif [ "$1" == "chunk" ]; then
+    elif [ "$1" = "chunk" ]; then
 	# ------------------ Chunks test ----------------------
 	# Split the dose and info files up into two chromosomes with
 	# some chunks
@@ -102,14 +102,21 @@
 }
 
 
-function run_test
+run_test ()
 {
     # Run an analysis on dosage data
     outfile="height_add.out.txt"
     rm -f $outfile
-    ./probabel.pl 1 2 linear TestCohortChunk --additive height
     echo "Checking output using dosages $WithOrWithout chunks..."
+    ./probabel.pl 1 2 linear $1 --additive height
+    echo -n "  Verifying $outfile"
     diff $outfile $results/$outfile
+    if [ $? == 0 ]; then
+	echo -e "\t\tOK"
+    else
+	echo -e "\t\tFAILED"
+	exit 1
+    fi
 
     # Run an analysis on probabilities
     outfilelist[1]="height_ngp2_2df.out.txt"
@@ -121,8 +128,8 @@
 	rm -f ${outfilelist[$i]}
     done
 
-    ./probabel.pl 1 2 linear TestCohortNoChunk --allmodels height -o _ngp2
     echo "Checking output using probabilities $WithOrWithout chunks..."
+    ./probabel.pl 1 2 linear $1 --allmodels height -o _ngp2
     for i in {1..5}; do
 	echo -n "  Verifying ${outfilelist[$i]}"
 	diff ${outfilelist[$i]} $results/${outfilelist[$i]}
@@ -130,6 +137,7 @@
 	    echo -e "\t\tOK"
 	else
 	    echo -e "\t\tFAILED"
+	    exit 1
 	fi
     done
 }
@@ -137,10 +145,10 @@
 # ---------- Continuation of the main function ----------
 prepare_input nochunk
 
-run_test
+run_test TestCohortNoChunk
 echo "-------------------- Finished check without chunks --------------------"
 
 prepare_input chunk
 
-run_test
+run_test TestCohortChunk
 echo "-------------------- Finished check with chunks --------------------"