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-rw-r--r--test/dev_test_suite.sh46
1 files changed, 46 insertions, 0 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
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+#!/usr/bin/env bash
+
+gemma=../bin/gemma
+
+testCenteredRelatednessMatrixKLOCO1() {
+    outn=mouse_hs1940_LOCO1
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+           -a ../example/mouse_hs1940.anno.txt -snps ../example/mouse_hs1940_snps.txt -nind 400 -loco 1 -gk -debug -o $outn
+    assertEquals 0 $?
+    grep "total computation time" < output/$outn.log.txt
+    outfn=output/$outn.cXX.txt
+    assertEquals 0 $?
+    assertEquals "400" `wc -l < $outfn`
+    assertEquals "0.312" `head -c 5 $outfn`
+    assertEquals "71.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+testUnivariateLinearMixedModelLOCO1() {
+    outn=mouse_hs1940_CD8_LOCO1_lmm
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+	   -n 1 \
+	   -loco 1 \
+           -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940_LOCO1.cXX.txt \
+	   -snps ../example/mouse_hs1940_snps.txt -lmm \
+	   -nind 400 \
+	   -debug \
+           -o $outn
+    assertEquals 0 $?
+    grep "total computation time" < output/$outn.log.txt
+    assertEquals 0 $?
+    outfn=output/$outn.assoc.txt
+    assertEquals "68" `wc -l < $outfn`
+    assertEquals "15465553.30" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+shunit2=`which shunit2`
+
+if [ -x "$shunit2" ]; then
+    echo run system shunit2
+    . $shunit2
+elif [ -e shunit2-2.0.3/src/shell/shunit2 ]; then
+    echo run shunit2 provided in gemma repo
+    . shunit2-2.0.3/src/shell/shunit2
+else
+    echo "Can not find shunit2 - see INSTALL.md"
+fi