diff options
Diffstat (limited to 'test/test_suite.sh')
| -rwxr-xr-x | test/test_suite.sh | 67 |
1 files changed, 33 insertions, 34 deletions
diff --git a/test/test_suite.sh b/test/test_suite.sh index 0991c63..44eb14c 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -8,9 +8,10 @@ testCenteredRelatednessMatrixKFullLOCO1() { -p ../example/mouse_hs1940.pheno.txt \ -a ../example/mouse_hs1940.anno.txt \ -loco 1 -gk -debug -o $outn - assertEquals 1 $? - # assertEquals "1940" `wc -l < $outfn` - # assertEquals "2246.57" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals 0 $? + outfn=output/$outn.cXX.txt + assertEquals "1940" `wc -l < $outfn` + assertEquals "2246.57" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testUnivariateLinearMixedModelFullLOCO1() { @@ -24,26 +25,24 @@ testUnivariateLinearMixedModelFullLOCO1() { -lmm \ -debug \ -o $outn - assertEquals 1 $? - # grep "total computation time" < output/$outn.log.txt - # assertEquals 0 $? - # outfn=output/$outn.assoc.txt - # assertEquals "951" `wc -l < $outfn` - # assertEquals "267509369.79" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals 0 $? + grep "total computation time" < output/$outn.log.txt + assertEquals 0 $? + outfn=output/$outn.assoc.txt + assertEquals "951" `wc -l < $outfn` + assertEquals "267509369.79" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testCenteredRelatednessMatrixK() { $gemma -g ../example/mouse_hs1940.geno.txt.gz \ -p ../example/mouse_hs1940.pheno.txt \ -gk -o mouse_hs1940 - assertEquals 1 $? - # grep "total computation time" < output/mouse_hs1940.log.txt - # assertEquals 1 $? - # outfn=output/mouse_hs1940.cXX.txt - # assertEquals "1940" `wc -l < $outfn` - # assertEquals "3763600" `wc -w < $outfn` - # assertEquals "0.335" `head -c 5 $outfn` - # assertEquals "1119.64" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals 0 $? + outfn=output/mouse_hs1940.cXX.txt + assertEquals "1940" `wc -l < $outfn` + assertEquals "3763600" `wc -w < $outfn` + assertEquals "0.335" `head -c 5 $outfn` + assertEquals "1119.64" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testUnivariateLinearMixedModel() { @@ -54,12 +53,12 @@ testUnivariateLinearMixedModel() { -k ./output/mouse_hs1940.cXX.txt \ -lmm \ -o mouse_hs1940_CD8_lmm - assertEquals 1 $? - # grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt - # assertEquals 0 $? - # outfn=output/mouse_hs1940_CD8_lmm.assoc.txt - # assertEquals "118459" `wc -w < $outfn` - # assertEquals "4038557453.62" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals 0 $? + grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt + assertEquals 0 $? + outfn=output/mouse_hs1940_CD8_lmm.assoc.txt + assertEquals "118459" `wc -w < $outfn` + assertEquals "4038557453.62" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testMultivariateLinearMixedModel() { @@ -69,11 +68,11 @@ testMultivariateLinearMixedModel() { -a ../example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940.cXX.txt \ -lmm -o mouse_hs1940_CD8MCH_lmm - assertEquals 1 $? + assertEquals 0 $? - # outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt - # assertEquals "139867" `wc -w < $outfn` - # assertEquals "4029037056.54" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt + assertEquals "139867" `wc -w < $outfn` + assertEquals "4029037056.54" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testPlinkStandardRelatednessMatrixK() { @@ -83,9 +82,9 @@ testPlinkStandardRelatednessMatrixK() { rm -f $outfn $gemma -bfile $datadir/HLC \ -gk 2 -o $testname - assertEquals 1 $? - # 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` + 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` } # Test for https://github.com/genetics-statistics/GEMMA/issues/58 @@ -99,10 +98,10 @@ testPlinkMultivariateLinearMixedModel() { -maf 0.1 \ -c $datadir/HLC_covariates.txt \ -o $testname - assertEquals 1 $? - # outfn=output/$testname.assoc.txt - # assertEquals "223243" `wc -l < $outfn` - # assertEquals "89756559859.06" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals 0 $? + outfn=output/$testname.assoc.txt + assertEquals "223243" `wc -l < $outfn` + assertEquals "89756559859.06" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } shunit2=`which shunit2` |