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| author | Peter Carbonetto | 2017-10-09 16:23:05 -0500 |
|---|---|---|
| committer | GitHub | 2017-10-09 16:23:05 -0500 |
| commit | ab2a1830659ac970d97c107f145105fb410eb219 (patch) | |
| tree | 14d3cab14fca4b68eb0916992344b8248a380a61 /test/dev_test_suite.sh | |
| parent | 1e99b37e42edb7981b44f1409cc3e55a47057878 (diff) | |
| parent | 86323ccaf26ad0a3b706a67a0014dd04b9965823 (diff) | |
| download | pangemma-ab2a1830659ac970d97c107f145105fb410eb219.tar.gz | |
Merge pull request #92 from genenetwork/gemma-master
Fixed for a number of outstanding issues.
Diffstat (limited to 'test/dev_test_suite.sh')
| -rwxr-xr-x | test/dev_test_suite.sh | 20 |
1 files changed, 11 insertions, 9 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 9e49251..0fc4423 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -2,7 +2,6 @@ gemma=../bin/gemma - # Related to https://github.com/genetics-statistics/GEMMA/issues/78 testBXDStandardRelatednessMatrixKSingularError() { outn=BXDerr @@ -32,7 +31,8 @@ testBXDStandardRelatednessMatrixK() { assertEquals "-116.11" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } -testBXDMultivariateLinearMixedModel() { +testBXDLMMLikelihoodRatio() { + outn=BXD_LMM_LR $gemma -g ../example/BXD_geno.txt.gz \ -p ../example/BXD_pheno.txt \ -c ../example/BXD_covariates2.txt \ @@ -40,12 +40,12 @@ testBXDMultivariateLinearMixedModel() { -k ./output/BXD.cXX.txt \ -lmm 2 -maf 0.1 \ -debug \ - -o BXD_mvlmm + -o $outn 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 }' $outfn` + outfn=output/$outn.assoc.txt + assertEquals "80498" `wc -w < $outfn` + assertEquals "3088458212.93" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testCenteredRelatednessMatrixKLOCO1() { @@ -65,10 +65,12 @@ testCenteredRelatednessMatrixKLOCO1() { testUnivariateLinearMixedModelLOCO1() { outn=mouse_hs1940_CD8_LOCO1_lmm rm -f output/$outn.* - $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ + $gemma -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_LOCO1.cXX.txt \ + -a ../example/mouse_hs1940.anno.txt \ + -k ./output/mouse_hs1940_LOCO1.cXX.txt \ -snps ../example/mouse_hs1940_snps.txt -lmm \ -nind 400 \ -debug \ @@ -78,7 +80,7 @@ testUnivariateLinearMixedModelLOCO1() { assertEquals 0 $? outfn=output/$outn.assoc.txt assertEquals "68" `wc -l < $outfn` - assertEquals "15465553.30" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } shunit2=`which shunit2` |