1#!/usr/bin/env bash 2# 3# Long running tests go here 4 5gemma=../bin/gemma 6export GSL_RNG_SEED=100 7 8testPlinkStandardRelatednessMatrixK() { 9 testname=testPlinkStandardRelatednessMatrixK 10 datadir=../example 11 outfn=output/$testname.sXX.txt 12 rm -f $outfn 13 $gemma -bfile $datadir/HLC \ 14 -gk 2 -o $testname \ 15 -debug 16 assertEquals 0 $? 17 assertEquals "427" `wc -l < $outfn` 18 assertEquals "-358.07" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` 19} 20 21testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() { 22 echo "Long running test!" 23 # This test passes, but takes over 30 minutes to run! 24 # n=2 is original pheno in fam file 25 # n=1 is causal1 26 # n=3..12 is causal2 27 # n=13..22 is causal3 28 # -n 1 2 3 15 is independent 29 testname=testPlinkMultivariateLinearMixedModelMultiplePhenotypes 30 datadir=../example 31 $gemma -bfile $datadir/HLC \ 32 -p $datadir/HLC.simu.pheno.txt \ 33 -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \ 34 -lmm 1 \ 35 -maf 0.1 \ 36 -n 1 2 3 15 \ 37 -c $datadir/HLC_covariates.txt \ 38 -debug \ 39 -o $testname 40 assertEquals 0 $? 41 outfn=output/$testname.assoc.txt 42 assertEquals "223243" `wc -l < $outfn` 43 assertEquals "89754977983.69" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` 44} 45 46shunit2=`which shunit2` 47 48if [ -x "$shunit2" ]; then 49 echo run system shunit2 50 . $shunit2 51elif [ -e ../contrib/shunit2-2.0.3/src/shell/shunit2 ]; then 52 echo run shunit2 provided in gemma repo 53 . ../contrib/shunit2-2.0.3/src/shell/shunit2 54else 55 echo "Can not find shunit2 - see INSTALL.md" 56fi 57