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#!/bin/sh
echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
gemma=../bin/gemma
gemmaopts="-debug"
export GSL_RNG_SEED=10
testBslmm1() {
outn=mouse_hs1940_CD8_bslmm
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 2 -a ../example/mouse_hs1940.anno.txt \
-bslmm -no-check \
-o $outn -w 1000 -s 10000 -seed 1
assertEquals 0 $?
outfn1=output/$outn.hyp.txt
outfn2=output/$outn.param.txt
# assertEquals "45181" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.0f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn1`
# assertEquals "4043967139.42" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn2`
}
testBslmm2() {
outn=mouse_hs1940_CD8_train
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 2 \
-a ../example/mouse_hs1940.anno.txt \
-gk 1 -o $outn
assertEquals 0 $?
outfn=output/$outn.cXX.txt
assertEquals "579.50" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBslmm3() {
## Fit a binary trait using a linear model
outn=mouse_hs1940_CD8_bslmm_cc1
$gemma $gemmaopts \
-g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 4 \
-a ../example/mouse_hs1940.anno.txt \
-bslmm \
-o $outn \
-w 1000 -s 10000 -seed 1 -no-check
assertEquals 0 $?
outfn=output/$outn.hyp.txt
# assertEquals "291" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.0f",(substr($x,,0,6))) } END { printf "%.0f",100*$sum }' $outfn`
}
testBslmm4() {
outn=mouse_hs1940_CD8_prdt_k
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 2 \
-epm ./output/mouse_hs1940_CD8_bslmm.param.txt \
-emu ./output/mouse_hs1940_CD8_bslmm.log.txt \
-ebv ./output/mouse_hs1940_CD8_bslmm.bv.txt \
-k ./output/mouse_hs1940_CD8_train.cXX.txt \
-predict -no-check \
-o $outn
assertEquals 0 $?
outfn=output/$outn.prdt.txt
# assertEquals "-60.33" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBslmm5() {
## Now, do prediction in the test set for the binary traits
## If the traits were fitted using the linear model, then:
outn=mouse_hs1940_CD8_prdt_cc1
$gemma $gemmaopts \
-g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 4 \
-epm ./output/mouse_hs1940_CD8_bslmm_cc1.param.txt \
-emu ./output/mouse_hs1940_CD8_bslmm_cc1.log.txt \
-predict \
-o $outn -seed 100
assertEquals 0 $?
outfn=output/$outn.prdt.txt
assertEquals "571.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testCenteredRelatednessMatrixKFullLOCO1() {
outn=mouse_hs1940_full_LOCO1
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-a ../example/mouse_hs1940.anno.txt \
-loco 1 -gk -o $outn
assertEquals 0 $?
outfn=output/$outn.cXX.txt
assertEquals "1940" `wc -l < $outfn`
assertEquals "2246.49" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testUnivariateLinearMixedModelFullLOCO1() {
outn=mouse_hs1940_CD8_full_LOCO1_lmm
$gemma $gemmaopts -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_full_LOCO1.cXX.txt \
-lmm -no-check \
-o $outn
assertEquals 0 $?
grep "total computation time" < output/$outn.log.txt
assertEquals 0 $?
outfn=output/$outn.assoc.txt
assertEquals "951" `wc -l < $outfn`
assertEquals "267507852.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testCenteredRelatednessMatrixK() {
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-gk -o mouse_hs1940
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 "1119.60" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testUnivariateLinearMixedModel() {
$gemma $gemmaopts -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 "129228" `wc -w < $outfn`
assertEquals "4038540440.81" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testLinearMixedModelPhenotypes() {
$gemma $gemmaopts -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 -no-check \
-o mouse_hs1940_CD8MCH_lmm
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
assertEquals "139867" `wc -w < $outfn`
assertEquals "4029037056.58" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testPlinkStandardRelatednessMatrixK() {
testname=testPlinkStandardRelatednessMatrixK
datadir=../example
outfn=output/$testname.sXX.txt
rm -f $outfn
$gemma $gemmaopts -bfile $datadir/HLC \
-gk 2 -o $testname
assertEquals 0 $?
assertEquals "427" `wc -l < $outfn`
assertEquals "-358.05" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
# Test for https://github.com/genetics-statistics/GEMMA/issues/58
# fixed GSLv2 NaN's that appeared with covariates.
testPlinkLinearMixedModelCovariates() {
testname=testPlinkLinearMixedModelCovariates
datadir=../example
$gemma $gemmaopts -bfile $datadir/HLC \
-k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
-lmm 1 \
-maf 0.1 \
-c $datadir/HLC_covariates.txt \
-no-check \
-o $testname
assertEquals 0 $?
outfn=output/$testname.assoc.txt
assertEquals "223243" `wc -l < $outfn`
assertEquals "89757159113.94" `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 ../contrib/shunit2-2.0.3/src/shell/shunit2 ]; then
echo run shunit2 provided in gemma repo
. ../contrib/shunit2-2.0.3/src/shell/shunit2
else
echo "Can not find shunit2 - see INSTALL.md"
fi
|
