diff options
Diffstat (limited to 'test/test_suite.sh')
| -rwxr-xr-x | test/test_suite.sh | 111 |
1 files changed, 91 insertions, 20 deletions
diff --git a/test/test_suite.sh b/test/test_suite.sh index 350fc27..7af33aa 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -1,13 +1,89 @@ #!/usr/bin/env bash gemma=../bin/gemma +gemmaopts="-debug" + +testBslmm1() { + outn=mouse_hs1940_CD8_bslmm + $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ + -p ../example/mouse_hs1940.pheno.txt \ + -n 2 -a ../example/mouse_hs1940.anno.txt \ + -bslmm \ + -o $outn -w 1000 -s 10000 -seed 1 + assertEquals 0 $? + outfn1=output/$outn.hyp.txt + outfn2=output/$outn.param.txt + # assertEquals "45181" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.0f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn1` + # assertEquals "4043967139.42" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn2` +} + +testBslmm2() { + outn=mouse_hs1940_CD8_train + $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ + -p ../example/mouse_hs1940.pheno.txt \ + -n 2 \ + -a ../example/mouse_hs1940.anno.txt \ + -gk 1 -o $outn + assertEquals 0 $? + outfn=output/$outn.cXX.txt + assertEquals "579.66" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + +testBslmm3() { + ## Fit a binary trait using a linear model + outn=mouse_hs1940_CD8_bslmm_cc1 + $gemma $gemmaopts \ + -g ../example/mouse_hs1940.geno.txt.gz \ + -p ../example/mouse_hs1940.pheno.txt \ + -n 4 \ + -a ../example/mouse_hs1940.anno.txt \ + -bslmm \ + -o $outn \ + -w 1000 -s 10000 -seed 1 + assertEquals 0 $? + outfn=output/$outn.hyp.txt + # assertEquals "291" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.0f",(substr($x,,0,6))) } END { printf "%.0f",100*$sum }' $outfn` +} + +testBslmm4() { + outn=mouse_hs1940_CD8_prdt_k + $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ + -p ../example/mouse_hs1940.pheno.txt \ + -n 2 \ + -epm ./output/mouse_hs1940_CD8_bslmm.param.txt \ + -emu ./output/mouse_hs1940_CD8_bslmm.log.txt \ + -ebv ./output/mouse_hs1940_CD8_bslmm.bv.txt \ + -k ./output/mouse_hs1940_CD8_train.cXX.txt \ + -predict \ + -o $outn + assertEquals 0 $? + outfn=output/$outn.prdt.txt + # assertEquals "-60.33" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + +testBslmm5() { + ## Now, do prediction in the test set for the binary traits + ## If the traits were fitted using the linear model, then: + outn=mouse_hs1940_CD8_prdt_cc1 + $gemma $gemmaopts \ + -g ../example/mouse_hs1940.geno.txt.gz \ + -p ../example/mouse_hs1940.pheno.txt \ + -n 4 \ + -epm ./output/mouse_hs1940_CD8_bslmm_cc1.param.txt \ + -emu ./output/mouse_hs1940_CD8_bslmm_cc1.log.txt \ + -predict \ + -o $outn + assertEquals 0 $? + outfn=output/$outn.prdt.txt + assertEquals "550.67" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} testCenteredRelatednessMatrixKFullLOCO1() { outn=mouse_hs1940_full_LOCO1 - $gemma -g ../example/mouse_hs1940.geno.txt.gz \ + $gemma $gemmaopts -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 + -loco 1 -gk -o $outn assertEquals 0 $? outfn=output/$outn.cXX.txt assertEquals "1940" `wc -l < $outfn` @@ -16,14 +92,13 @@ testCenteredRelatednessMatrixKFullLOCO1() { testUnivariateLinearMixedModelFullLOCO1() { outn=mouse_hs1940_CD8_full_LOCO1_lmm - $gemma -g ../example/mouse_hs1940.geno.txt.gz \ + $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_full_LOCO1.cXX.txt \ -lmm \ - -debug \ -o $outn assertEquals 0 $? grep "total computation time" < output/$outn.log.txt @@ -34,9 +109,9 @@ testUnivariateLinearMixedModelFullLOCO1() { } testCenteredRelatednessMatrixK() { - $gemma -g ../example/mouse_hs1940.geno.txt.gz \ + $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ -p ../example/mouse_hs1940.pheno.txt \ - -gk -o mouse_hs1940 -debug + -gk -o mouse_hs1940 assertEquals 0 $? outfn=output/mouse_hs1940.cXX.txt assertEquals "1940" `wc -l < $outfn` @@ -46,14 +121,13 @@ testCenteredRelatednessMatrixK() { } testUnivariateLinearMixedModel() { - $gemma -g ../example/mouse_hs1940.geno.txt.gz \ + $gemma $gemmaopts -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 + -o mouse_hs1940_CD8_lmm assertEquals 0 $? grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt assertEquals 0 $? @@ -62,14 +136,13 @@ testUnivariateLinearMixedModel() { assertEquals "4038540440.86" `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 \ +testLinearMixedModelPhenotypes() { + $gemma $gemmaopts -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 + -lmm -o mouse_hs1940_CD8MCH_lmm assertEquals 0 $? outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt @@ -82,9 +155,8 @@ testPlinkStandardRelatednessMatrixK() { datadir=../example outfn=output/$testname.sXX.txt rm -f $outfn - $gemma -bfile $datadir/HLC \ - -gk 2 -o $testname \ - -debug + $gemma $gemmaopts -bfile $datadir/HLC \ + -gk 2 -o $testname 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` @@ -92,15 +164,14 @@ testPlinkStandardRelatednessMatrixK() { # Test for https://github.com/genetics-statistics/GEMMA/issues/58 # fixed GSLv2 NaN's that appeared with covariates. -testPlinkMultivariateLinearMixedModel() { - testname=testPlinkMultivariateLinearMixedModel +testPlinkLinearMixedModelCovariates() { + testname=testPlinkLinearMixedModelCovariates datadir=../example - $gemma -bfile $datadir/HLC \ + $gemma $gemmaopts -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 |