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| author | Pjotr Prins | 2017-10-05 09:18:59 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2017-10-05 09:19:09 +0000 |
| commit | 530488454ae6a35b098b81b45581f88f02d6de0e (patch) | |
| tree | 7ee31c78a678ea4fa364267a9de8564faf4b159e /test/test_suite.sh | |
| parent | e90c2d25cdb77d41d6587188db9e61cb988f2c78 (diff) | |
| download | pangemma-530488454ae6a35b098b81b45581f88f02d6de0e.tar.gz | |
Adding debug statements on entering functions and added test for issue 58
Diffstat (limited to 'test/test_suite.sh')
| -rwxr-xr-x | test/test_suite.sh | 35 |
1 files changed, 31 insertions, 4 deletions
diff --git a/test/test_suite.sh b/test/test_suite.sh index 44eb14c..fa66b7a 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -36,7 +36,7 @@ testUnivariateLinearMixedModelFullLOCO1() { testCenteredRelatednessMatrixK() { $gemma -g ../example/mouse_hs1940.geno.txt.gz \ -p ../example/mouse_hs1940.pheno.txt \ - -gk -o mouse_hs1940 + -gk -o mouse_hs1940 -debug assertEquals 0 $? outfn=output/mouse_hs1940.cXX.txt assertEquals "1940" `wc -l < $outfn` @@ -52,7 +52,8 @@ testUnivariateLinearMixedModel() { -a ../example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940.cXX.txt \ -lmm \ - -o mouse_hs1940_CD8_lmm + -o mouse_hs1940_CD8_lmm \ + -debug assertEquals 0 $? grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt assertEquals 0 $? @@ -67,7 +68,8 @@ testMultivariateLinearMixedModel() { -n 1 6 \ -a ../example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940.cXX.txt \ - -lmm -o mouse_hs1940_CD8MCH_lmm + -lmm -o mouse_hs1940_CD8MCH_lmm \ + -debug assertEquals 0 $? outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt @@ -81,7 +83,8 @@ testPlinkStandardRelatednessMatrixK() { outfn=output/$testname.sXX.txt rm -f $outfn $gemma -bfile $datadir/HLC \ - -gk 2 -o $testname + -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` @@ -97,6 +100,30 @@ testPlinkMultivariateLinearMixedModel() { -lmm 1 \ -maf 0.1 \ -c $datadir/HLC_covariates.txt \ + -debug \ + -o $testname + 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` +} + +testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() { + # 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 |