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| author | Pjotr Prins | 2017-08-26 07:41:48 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2017-08-26 09:38:00 +0000 |
| commit | ea21ba73273891261ba2e4d0d85729f308c54d72 (patch) | |
| tree | a789922ea2fc313f17fae9c2c493fda043d61755 /test | |
| parent | 43dc1c9519aac4924d1174f265fdcac7b7791f8e (diff) | |
| download | pangemma-ea21ba73273891261ba2e4d0d85729f308c54d72.tar.gz | |
Tests and enforces added related to https://github.com/genetics-statistics/GEMMA/issues/78
Diffstat (limited to 'test')
| -rwxr-xr-x | test/dev_test_suite.sh | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 0b65c1e..67d9cba 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -2,6 +2,50 @@ gemma=../bin/gemma + +# Related to https://github.com/genetics-statistics/GEMMA/issues/78 +testBXDStandardRelatednessMatrixKSingularError() { + outn=BXDerr + rm -f output/$outn.* + $gemma -g ../example/BXD_geno.txt.gz \ + -p ../example/BXD_pheno.txt \ + -c ../example/BXD_covariates.txt \ + -a ../example/BXD_snps.txt \ + -gk \ + -debug -o $outn + assertEquals 22 $? # should show singular error +} + +testBXDStandardRelatednessMatrixK() { + outn=BXD + rm -f output/$outn.* + $gemma -g ../example/BXD_geno.txt.gz \ + -p ../example/BXD_pheno.txt \ + -c ../example/BXD_covariates2.txt \ + -a ../example/BXD_snps.txt \ + -gk \ + -debug -o $outn + assertEquals 0 $? + outfn=output/$outn.cXX.txt + assertEquals "198" `wc -l < $outfn` + assertEquals "-116.11" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + +testBXDMultivariateLinearMixedModel() { + $gemma -g ../example/BXD_geno.txt.gz \ + -p ../example/BXD_pheno.txt \ + -c ../example/BXD_covariates2.txt \ + -a ../example/BXD_snps.txt \ + -k ./output/BXD.cXX.txt \ + -lmm 2 -maf 0.1 \ + -o BXD_mvlmm + assertEquals 0 $? + + outfn=output/BXD_mvlmm.assoc.txt + assertEquals "65862" `wc -w < $outfn` + assertEquals "3088489421.94" `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.* |