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| author | Pjotr Prins | 2017-10-20 08:10:39 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2017-10-23 13:54:05 +0000 |
| commit | b42a02d02b3d9384b1da55bd091f0f89c808b626 (patch) | |
| tree | 4fd66b70ce7eb660dcb98c38a7f5309ac43195e8 /test | |
| parent | 12558c358150bfed99874b791932bbe06a107263 (diff) | |
| download | pangemma-b42a02d02b3d9384b1da55bd091f0f89c808b626.tar.gz | |
Travis-ci:
- Disabled gcc-6 since we develop with later tools anyway - Turned the release test into a simple integration test - Adding MacOSX on Travis-ci Tests: Adding tests for Plink w. LOCO Safety: Introduce strtok_safe to get rid of segfaults
Diffstat (limited to 'test')
| -rwxr-xr-x | test/dev_test_suite.sh | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 77604be..284c9aa 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -84,6 +84,49 @@ testUnivariateLinearMixedModelLOCO1() { assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } +testPlinkCenteredRelatednessMatrixKLOCO1() { + return 0 + outn=mouse_hs1940_Plink_LOCO1 + rm -f output/$outn.* + $gemma -bfile ../example/mouse_hs1940 \ + -a ../example/mouse_hs1940.anno.txt \ + -snps ../example/mouse_hs1940_snps.txt \ + -nind 400 \ + -loco 1 \ + -gk \ + -debug \ + -o $outn + assertEquals 0 $? + grep "total computation time" < output/$outn.log.txt + outfn=output/$outn.cXX.txt + assertEquals 0 $? + assertEquals "400" `wc -l < $outfn` + assertEquals "0.312" `head -c 5 $outfn` + assertEquals "71.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + + +testPlinkUnivariateLinearMixedModelLOCO1() { + return 0 + outn=mouse_hs1940_CD8_Plink_LOCO1_lmm + rm -f output/$outn.* + $gemma -bfile ../example/mouse_hs1940 \ + -n 1 \ + -loco 1 \ + -k ./output/mouse_hs1940_Plink_LOCO1.cXX.txt \ + -a ../example/mouse_hs1940.anno.txt \ + -snps ../example/mouse_hs1940_snps.txt -lmm \ + -nind 400 \ + -debug \ + -o $outn + assertEquals 0 $? + grep "total computation time" < output/$outn.log.txt + assertEquals 0 $? + outfn=output/$outn.assoc.txt + assertEquals "68" `wc -l < $outfn` + assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + shunit2=`which shunit2` if [ -x "$shunit2" ]; then |