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#!/usr/bin/env bash
#
# Long running tests go here
gemma=../bin/gemma
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`
}
testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() {
echo "Long running test!"
# This test passes, but takes over 30 minutes to run!
# 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 "89754977983.69" `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
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