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#!/usr/bin/env bash
gemma=../bin/gemma
testCenteredRelatednessMatrixKFullLOCO1() {
outn=mouse_hs1940_full_LOCO1
$gemma -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-a ../example/mouse_hs1940.anno.txt \
-loco 1 -gk -debug -o $outn
assertEquals 0 $?
outfn=output/$outn.cXX.txt
assertEquals "1940" `wc -l < $outfn`
assertEquals "2246.57" `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 -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 \
-debug \
-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 "267509369.79" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testCenteredRelatednessMatrixK() {
$gemma -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-gk -o mouse_hs1940 -debug
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 "1119.64" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$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 \
-debug
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 "4038557453.62" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$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 \
-debug
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
assertEquals "139867" `wc -w < $outfn`
assertEquals "4029037056.54" `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 -bfile $datadir/HLC \
-gk 2 -o $testname \
-debug
assertEquals 0 $?
assertEquals "427" `wc -l < $outfn`
assertEquals "-358.07" `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.
testPlinkMultivariateLinearMixedModel() {
testname=testPlinkMultivariateLinearMixedModel
datadir=../example
$gemma -bfile $datadir/HLC \
-k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
-lmm 1 \
-maf 0.1 \
-c $datadir/HLC_covariates.txt \
-debug \
-o $testname
assertEquals 0 $?
outfn=output/$testname.assoc.txt
assertEquals "223243" `wc -l < $outfn`
assertEquals "89756559859.06" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() {
# n=2 is original pheno in fam file
# n=1 is causal1
# n=3..12 is causal2
# n=13..22 is causal3
# -n 1 2 3 15 is independent
testname=testPlinkMultivariateLinearMixedModelMultiplePhenotypes
datadir=../example
$gemma -bfile $datadir/HLC \
-p $datadir/HLC.simu.pheno.txt \
-k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
-lmm 1 \
-maf 0.1 \
-n 1 2 3 15 \
-c $datadir/HLC_covariates.txt \
-debug \
-o $testname
assertEquals 0 $?
outfn=output/$testname.assoc.txt
assertEquals "223243" `wc -l < $outfn`
assertEquals "89756559859.06" `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
|
