diff options
Diffstat (limited to 'test')
| -rwxr-xr-x | test/dev_test_suite.sh | 2 | ||||
| -rw-r--r-- | test/dev_tests.rb | 34 | ||||
| -rwxr-xr-x | test/lengthy_test_suite.sh | 2 | ||||
| -rw-r--r-- | test/lib/test-helpers.rb | 14 | ||||
| -rwxr-xr-x | test/test_suite.sh | 2 |
5 files changed, 42 insertions, 12 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 676e0b3..a5ec3f4 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -1,5 +1,7 @@ #!/bin/sh +echo "WARNING: THIS TEST SUITE IS NO LONGER USED" + gemma=../bin/gemma # gemmaopts="-debug -strict" gemmaopts="-debug -check" diff --git a/test/dev_tests.rb b/test/dev_tests.rb index fb3fecf..fc2f7bb 100644 --- a/test/dev_tests.rb +++ b/test/dev_tests.rb @@ -10,7 +10,7 @@ class TestQuick < MiniTest::Test end def test_linear_model - assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + gemma("-g ./example/mouse_hs1940.geno.txt.gz \ -p ./example/mouse_hs1940.pheno.txt \ -n 1 \ -a ./example/mouse_hs1940.anno.txt \ @@ -23,14 +23,14 @@ class TestQuick < MiniTest::Test end def test_BXD - assert gemma("-g ./example/BXD_geno.txt.gz \ + gemma("-g ./example/BXD_geno.txt.gz \ -p ./example/BXD_pheno.txt \ -c ./example/BXD_covariates2.txt \ -a ./example/BXD_snps.txt \ -gk \ -o BXD") - assert gemma("-g ./example/BXD_geno.txt.gz \ + gemma("-g ./example/BXD_geno.txt.gz \ -p ./example/BXD_pheno.txt \ -c ./example/BXD_covariates2.txt \ -a ./example/BXD_snps.txt \ @@ -39,18 +39,18 @@ class TestQuick < MiniTest::Test -o BXDLMM") expect("output/BXDLMM.assoc.txt",[[2,9,"1.234747e-01"], - [:max,9,"9.997119e-01"]]) + [:max,"p_lrt","9.997119e-01"]]) end def test_mouse_hs1940_loco - assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + 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 \ -o mouse_hs1940_loco") - assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + gemma("-g ./example/mouse_hs1940.geno.txt.gz \ -p ./example/mouse_hs1940.pheno.txt \ -n 1 \ -loco 1 \ @@ -61,6 +61,26 @@ class TestQuick < MiniTest::Test -nind 400 -no-check \ -o mouse_hs1940_loco") expect("output/mouse_hs1940_loco.assoc.txt",[[2,9,"-3.073643e+02"], - [:max,11,"9.716047e-01"]]) + [:max,"p_wald","9.716047e-01"]]) end + + # Test for https://github.com/genetics-statistics/GEMMA/issues/58 + # fixed GSLv2 NaN's that appeared with covariates. + def test_plink_covariates_lmm + gemma("-bfile example/HLC -gk 2 -o testPlinkStandardRelatednessMatrixK") + + gemma("-bfile example/HLC \ + -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \ + -lmm 1 \ + -maf 0.1 \ + -c example/HLC_covariates.txt \ + -no-check \ + -o plink_lmm1_cov") + expect("output/plink_lmm1_cov.assoc.txt",[[100,"p_wald","5.189953e-01"], + [:max,"logl_H1","279.2689"], + [:max,"l_remle","1.686062"], + [:max,"p_wald","0.9999996"]]) + end + + end diff --git a/test/lengthy_test_suite.sh b/test/lengthy_test_suite.sh index 6e93220..6e11793 100755 --- a/test/lengthy_test_suite.sh +++ b/test/lengthy_test_suite.sh @@ -2,6 +2,8 @@ # # Long running tests go here +echo "WARNING: THIS TEST SUITE IS NO LONGER USED" + gemma=../bin/gemma export GSL_RNG_SEED=100 diff --git a/test/lib/test-helpers.rb b/test/lib/test-helpers.rb index d2989e0..672a2c2 100644 --- a/test/lib/test-helpers.rb +++ b/test/lib/test-helpers.rb @@ -2,7 +2,7 @@ module TestHelpers # Runs gemma and returns true if successful def gemma(opts) - system("./bin/gemma #{opts}") + assert system("./bin/gemma #{opts}") end def read(fn, line=0) @@ -18,11 +18,15 @@ module TestHelpers lines = lines.map { |l| l.split("\t") } # avoid this for large files list.each do | l | line,colnum,value = l - if line == :max - cols = lines.max_by {|a| a[colnum].to_f} - else - cols = lines[line] + if colnum.is_a? String + colnum = lines[0].index(colnum) end + cols = + if line == :max + lines.max_by {|a| a[colnum].to_f} + else + lines[line] + end # assert_equal value,cols[colnum] assert_in_delta value.to_f,cols[colnum].to_f, 0.001 end diff --git a/test/test_suite.sh b/test/test_suite.sh index cc244c0..38671be 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -1,5 +1,7 @@ #!/bin/sh +echo "WARNING: THIS TEST SUITE IS NO LONGER USED" + gemma=../bin/gemma gemmaopts="-debug" export GSL_RNG_SEED=10 |