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| author | Pjotr Prins | 2017-08-14 07:43:07 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2017-08-14 08:23:14 +0000 |
| commit | ff1252fe3db1ba639fe148f45b0408a4f182da0d (patch) | |
| tree | e11ee6858159b53b2570273f9ba3d1ac882232f7 /test/dev_test_suite.sh | |
| parent | 3763f477e17a74942e1bf545aa9493d39bf9448e (diff) | |
| download | pangemma-ff1252fe3db1ba639fe148f45b0408a4f182da0d.tar.gz | |
Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26
Diffstat (limited to 'test/dev_test_suite.sh')
| -rwxr-xr-x | test/dev_test_suite.sh | 19 |
1 files changed, 19 insertions, 0 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 522cf3d..fb88e9d 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -2,8 +2,26 @@ gemma=../bin/gemma +# Test for https://github.com/genetics-statistics/GEMMA/issues/26 +# Always getting 'pve estimate =0.99xxx se(pve) =-nan' +testIssue26() { + outn=issue26 + rm -f output/$outn.* + $gemma -bfile data/issue26/mydata -k data/issue26/mydata_kinship.sXX.txt \ + -miss 1 -maf 0.01 -r2 1 -lmm \ + -debug -issue 26 \ + -o $outn + assertEquals 0 $? + outfn=output/$outn.assoc.txt + grep "total computation time" < output/$outn.log.txt + assertEquals 0 $? + assertEquals "2001" `wc -l < $outfn` + assertEquals "1582899231.18" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + testCenteredRelatednessMatrixKLOCO1() { outn=mouse_hs1940_LOCO1 + rm -f output/$outn.* $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ -a ../example/mouse_hs1940.anno.txt -snps ../example/mouse_hs1940_snps.txt -nind 400 -loco 1 -gk -debug -o $outn assertEquals 0 $? @@ -17,6 +35,7 @@ testCenteredRelatednessMatrixKLOCO1() { testUnivariateLinearMixedModelLOCO1() { outn=mouse_hs1940_CD8_LOCO1_lmm + rm -f output/$outn.* $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ -n 1 \ -loco 1 \ |