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#!/usr/bin/env bash
gemma=../bin/gemma
# Test for https://github.com/genetics-statistics/GEMMA/issues/26
# Always getting 'pve estimate =0.99xxx se(pve) =-nan'
testIssue26() {
outn=issue26
rm -f output/$outn.*
$gemma -bfile data/issue26/mydata -k data/issue26/mydata_kinship.sXX.txt \
-miss 1 -maf 0.01 -r2 1 -lmm \
-debug -issue 26 \
-o $outn
assertEquals 0 $?
outfn=output/$outn.assoc.txt
grep "total computation time" < output/$outn.log.txt
assertEquals 0 $?
assertEquals "2001" `wc -l < $outfn`
assertEquals "1582899231.18" `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 -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 }' $outfn`
}
testUnivariateLinearMixedModelLOCO1() {
outn=mouse_hs1940_CD8_LOCO1_lmm
rm -f output/$outn.*
$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
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