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|
#!/usr/bin/env bash
gemma=../bin/gemma
# gemmaopts="-debug -strict"
gemmaopts="-debug"
testLinearModel() {
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 1 \
-a ../example/mouse_hs1940.anno.txt \
-lm \
-o mouse_hs1940_CD8_lm
assertEquals 0 $?
grep "total computation time" < output/mouse_hs1940_CD8_lm.log.txt
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8_lm.assoc.txt
assertEquals "118459" `wc -w < $outfn`
assertEquals "4053667109.69" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
# Related to https://github.com/genetics-statistics/GEMMA/issues/78
testBXDStandardRelatednessMatrixKSingularError() {
outn=BXDerr
rm -f output/$outn.*
$gemma $gemmaopts \
-g ../example/BXD_geno.txt.gz \
-p ../example/BXD_pheno.txt \
-c ../example/BXD_covariates.txt \
-a ../example/BXD_snps.txt \
-gk \
-no-check \
-o $outn
assertEquals 22 $? # should show singular error
}
testBXDStandardRelatednessMatrixK() {
outn=BXD
rm -f output/$outn.*
$gemma $gemmaopts -g ../example/BXD_geno.txt.gz \
-p ../example/BXD_pheno.txt \
-c ../example/BXD_covariates2.txt \
-a ../example/BXD_snps.txt \
-gk \
-o $outn
assertEquals 0 $?
outfn=output/$outn.cXX.txt
assertEquals "198" `wc -l < $outfn`
assertEquals "-116.11" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBXDLMLikelihoodRatio() {
outn=BXD_LM_LR
$gemma $gemmaopts -g ../example/BXD_geno.txt.gz \
-p ../example/BXD_pheno.txt \
-c ../example/BXD_covariates2.txt \
-a ../example/BXD_snps.txt \
-k ./output/BXD.cXX.txt \
-lm 4 -maf 0.1 \
-o $outn
assertEquals 0 $?
outfn=output/$outn.assoc.txt
assertEquals "95134" `wc -w < $outfn`
assertEquals "3089042886.28" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBXDLMMLikelihoodRatio() {
outn=BXD_LMM_LR
$gemma $gemmaopts -g ../example/BXD_geno.txt.gz \
-p ../example/BXD_pheno.txt \
-c ../example/BXD_covariates2.txt \
-a ../example/BXD_snps.txt \
-k ./output/BXD.cXX.txt \
-lmm 2 -no-check -maf 0.1 \
-o $outn
assertEquals 0 $?
outfn=output/$outn.assoc.txt
assertEquals "73180" `wc -w < $outfn`
assertEquals "3088458212.93" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testCenteredRelatednessMatrixKLOCO1() {
outn=mouse_hs1940_LOCO1
rm -f output/$outn.*
$gemma $gemmaopts -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 -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 }' $outfn`
}
testUnivariateLinearMixedModelLOCO1() {
outn=mouse_hs1940_CD8_LOCO1_lmm
rm -f output/$outn.*
$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_LOCO1.cXX.txt \
-snps ../example/mouse_hs1940_snps.txt -lmm \
-nind 400 -no-check \
-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 "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testPlinkCenteredRelatednessMatrixKLOCO1() {
return 0
outn=mouse_hs1940_Plink_LOCO1
rm -f output/$outn.*
$gemma $gemmaopts -bfile ../example/mouse_hs1940 \
-a ../example/mouse_hs1940.anno.txt \
-snps ../example/mouse_hs1940_snps.txt \
-nind 400 \
-loco 1 \
-gk \
-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 }' $outfn`
}
testPlinkUnivariateLinearMixedModelLOCO1() {
return 0
outn=mouse_hs1940_CD8_Plink_LOCO1_lmm
rm -f output/$outn.*
$gemma $gemmaopts -bfile ../example/mouse_hs1940 \
-n 1 \
-loco 1 \
-k ./output/mouse_hs1940_Plink_LOCO1.cXX.txt \
-a ../example/mouse_hs1940.anno.txt \
-snps ../example/mouse_hs1940_snps.txt -lmm \
-nind 400 \
-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 "15465346.22" `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
|
