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#!/usr/bin/env bash
gemma=../bin/gemma
testCenteredRelatednessMatrixK() {
$gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
-a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940
assertEquals 0 $?
grep "total computation time" < output/mouse_hs1940.log.txt
assertEquals 0 $?
outfn=output/mouse_hs1940.cXX.txt
assertEquals "1940" `wc -l < $outfn`
assertEquals "3763600" `wc -w < $outfn`
assertEquals "0.335" `head -c 5 $outfn`
assertEquals "24.9799" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
}
testUnivariateLinearMixedModel() {
$gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -n 1 \
-a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm \
-o mouse_hs1940_CD8_lmm
assertEquals 0 $?
grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8_lmm.assoc.txt
assertEquals "118459" `wc -w < $outfn`
assertEquals "92047" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
}
testMultivariateLinearMixedModel() {
$gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
-n 1 6 -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \
-lmm -o mouse_hs1940_CD8MCH_lmm
assertEquals 0 $?
grep "total computation time" < output/mouse_hs1940_CD8MCH_lmm.log.txt
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
assertEquals "139867" `wc -w < $outfn`
assertEquals "92079" `perl -nle '$sum += substr($_,0,6) } END { print $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
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