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commit c8563e48d23f4545fdf954c50096347761f533dd Author: Dylan Aïssi <[email protected]> Date: Thu Dec 18 18:58:15 2014 +0100 Added tests --- debian/control | 1 + debian/tests/control | 2 ++ debian/tests/run-sample-analysis | 31 ++++++++++++++++++++++ debian/upstream.docs/samples/output/README | 11 ++++++++ debian/upstream.docs/samples/output/fixed.err.out | 3 +++ debian/upstream.docs/samples/output/fixed.gc.out | 1 + debian/upstream.docs/samples/output/fixed.log.out | 13 +++++++++ debian/upstream.docs/samples/output/fixed.out | 13 +++++++++ debian/upstream.docs/samples/output/random.err.out | 3 +++ debian/upstream.docs/samples/output/random.gc.out | 1 + debian/upstream.docs/samples/output/random.log.out | 13 +++++++++ debian/upstream.docs/samples/output/random.out | 13 +++++++++ 12 files changed, 105 insertions(+) diff --git a/debian/control b/debian/control index b0cffcd..d700569 100644 --- a/debian/control +++ b/debian/control @@ -5,6 +5,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Dylan Aïssi <[email protected]> Build-Depends: debhelper (>= 9), zlib1g-dev +Testsuite: autopkgtest Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/gwama.git Vcs-Git: git://anonscm.debian.org/debian-med/gwama.git diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 0000000..3403f8a --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,2 @@ +Tests: run-sample-analysis +Depends: @ diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis new file mode 100644 index 0000000..4cc1015 --- /dev/null +++ b/debian/tests/run-sample-analysis @@ -0,0 +1,31 @@ +#!/bin/sh -e +# http://dep.debian.net/deps/dep8/ +# Autopkgtest: Test if GWAMA run analysis correctly +# Author: Dylan Aïssi <[email protected]> +# Last-Update: 2014-12-18 + +pkg=gwama +if [ "$ADTTMP" = "" ] ; then + ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi +cd $ADTTMP +cp -a /usr/share/doc/${pkg}/examples/samples/* $ADTTMP + +GWAMA_TEST='GWAMA --filelist "gwama.in" --quantitative' + +# Fixed analysis +$GWAMA_TEST --output "test_fixed" +diff test_fixed.out output/fixed.out +diff test_fixed.log.out output/fixed.log.out +diff test_fixed.gc.out output/fixed.gc.out +diff test_fixed.err.out output/fixed.err.out + +# Random analysis +$GWAMA_TEST --output "test_random" --random +diff test_random.out output/random.out +diff test_random.log.out output/random.log.out +diff test_random.gc.out output/random.gc.out +diff test_random.err.out output/random.err.out + +rm -f $ADTTMP/* + diff --git a/debian/upstream.docs/samples/output/README b/debian/upstream.docs/samples/output/README new file mode 100644 index 0000000..30cd164 --- /dev/null +++ b/debian/upstream.docs/samples/output/README @@ -0,0 +1,11 @@ +# *.out files were generated following: + +wget http://www.well.ox.ac.uk/gwama/gwama2.1.zip +unzip gwama2.1.zip +make + +wget http://www.well.ox.ac.uk/gwama/samples.zip +unzip samples.zip + +./GWAMA --filelist "gwama.in" --output "fixed" --quantitative +./GWAMA --filelist "gwama.in" --output "random" --quantitative --random diff --git a/debian/upstream.docs/samples/output/fixed.err.out b/debian/upstream.docs/samples/output/fixed.err.out new file mode 100644 index 0000000..b257341 --- /dev/null +++ b/debian/upstream.docs/samples/output/fixed.err.out @@ -0,0 +1,3 @@ +E000000001 pop1.txt has problem with odds ratio or its CI of rs2905035! +E000000001 pop1.txt Given values: BETA=-0.0435863 SE=NA. Marker not used! +E000000002 pop3.txt error: Marker rs12138618 has wrong alleles. Marker dropped. diff --git a/debian/upstream.docs/samples/output/fixed.gc.out b/debian/upstream.docs/samples/output/fixed.gc.out new file mode 100644 index 0000000..1d5b754 --- /dev/null +++ b/debian/upstream.docs/samples/output/fixed.gc.out @@ -0,0 +1 @@ +Cohort directly_genotyped_markers_lambda directly_genotyped_markers_count imputed_markers_lambda imputed_markers_count diff --git a/debian/upstream.docs/samples/output/fixed.log.out b/debian/upstream.docs/samples/output/fixed.log.out new file mode 100644 index 0000000..cab0776 --- /dev/null +++ b/debian/upstream.docs/samples/output/fixed.log.out @@ -0,0 +1,13 @@ +Running GWAMA 2.1 +Reading input file list: + pop1.txt + pop2.txt + pop3.txt +END-OF-FILE +Study count: 3 + [1] Reading file: pop1.txt +pop1.txt has problem with beta and se for marker rs2905035!(E000000001) + [2] Reading file: pop2.txt + [3] Reading file: pop3.txt +Error: Marker rs12138618 has wrong alleles. (E000000002) +Analysis finished. diff --git a/debian/upstream.docs/samples/output/fixed.out b/debian/upstream.docs/samples/output/fixed.out new file mode 100644 index 0000000..2185102 --- /dev/null +++ b/debian/upstream.docs/samples/output/fixed.out @@ -0,0 +1,13 @@ +rs_number reference_allele other_allele eaf beta se beta_95L beta_95U z p-value _-log10_p-value q_statistic q_p-value i2 n_studies n_samples effects +rs12565286 G C -9 -0.008286 0.234417 -0.467743 0.451172 -0.035346 0.971791 0.012427 0.003670 0.998166 0.000000 3 -9 -+- +rs2977670 C G -9 -0.005583 0.234719 -0.465633 0.454467 -0.023785 0.981014 0.008325 0.002566 0.998718 0.000000 3 -9 -+- +rs12138618 G A -9 -0.301597 0.263780 -0.818606 0.215413 -1.143363 0.252868 0.597106 0.743322 0.388599 0.000000 2 -9 --? +rs3094315 G A -9 0.024358 0.059839 -0.092925 0.141642 0.407069 0.683975 0.164960 0.001125 0.999438 0.000000 3 -9 +++ +rs3131968 G A -9 -0.232347 0.058760 -0.347517 -0.117178 -3.954188 7.75E-05 4.110422 5.384402 0.067732 0.628557 3 -9 --- +rs2519016 T C -9 0.245651 0.211583 -0.169052 0.660354 1.161015 0.245616 0.609744 0.005762 0.997123 0.000000 3 -9 +++ +rs12562034 G A -9 0.009251 0.161478 -0.307246 0.325748 0.057292 0.954295 0.020317 0.000000 1.000000 0.000000 3 -9 +++ +rs12124819 A G -9 0.026341 0.086684 -0.143560 0.196243 0.303875 0.761227 0.118486 0.000001 0.999080 0.000000 2 -9 ++? +rs2980319 T A -9 -0.036137 0.062362 -0.158367 0.086093 -0.579476 0.562290 0.250039 0.034755 0.982773 0.000000 3 -9 --- +rs4040617 A G -9 0.008662 0.058561 -0.106118 0.123443 0.147921 0.882386 0.054341 0.434761 0.804624 0.000000 3 -9 ++- +rs11804171 T A -9 -0.002144 0.287772 -0.566177 0.561889 -0.007450 0.994052 0.002591 0.002162 0.962916 0.000000 2 -9 ?+- +rs2905035 G A -9 -0.044114 0.071935 -0.185107 0.096880 -0.613241 0.539737 0.267817 0.001595 0.968147 0.000000 2 -9 ?-- diff --git a/debian/upstream.docs/samples/output/random.err.out b/debian/upstream.docs/samples/output/random.err.out new file mode 100644 index 0000000..b257341 --- /dev/null +++ b/debian/upstream.docs/samples/output/random.err.out @@ -0,0 +1,3 @@ +E000000001 pop1.txt has problem with odds ratio or its CI of rs2905035! +E000000001 pop1.txt Given values: BETA=-0.0435863 SE=NA. Marker not used! +E000000002 pop3.txt error: Marker rs12138618 has wrong alleles. Marker dropped. diff --git a/debian/upstream.docs/samples/output/random.gc.out b/debian/upstream.docs/samples/output/random.gc.out new file mode 100644 index 0000000..1d5b754 --- /dev/null +++ b/debian/upstream.docs/samples/output/random.gc.out @@ -0,0 +1 @@ +Cohort directly_genotyped_markers_lambda directly_genotyped_markers_count imputed_markers_lambda imputed_markers_count diff --git a/debian/upstream.docs/samples/output/random.log.out b/debian/upstream.docs/samples/output/random.log.out new file mode 100644 index 0000000..cab0776 --- /dev/null +++ b/debian/upstream.docs/samples/output/random.log.out @@ -0,0 +1,13 @@ +Running GWAMA 2.1 +Reading input file list: + pop1.txt + pop2.txt + pop3.txt +END-OF-FILE +Study count: 3 + [1] Reading file: pop1.txt +pop1.txt has problem with beta and se for marker rs2905035!(E000000001) + [2] Reading file: pop2.txt + [3] Reading file: pop3.txt +Error: Marker rs12138618 has wrong alleles. (E000000002) +Analysis finished. diff --git a/debian/upstream.docs/samples/output/random.out b/debian/upstream.docs/samples/output/random.out new file mode 100644 index 0000000..a7fba6d --- /dev/null +++ b/debian/upstream.docs/samples/output/random.out @@ -0,0 +1,13 @@ +rs_number reference_allele other_allele eaf beta se beta_95L beta_95U z p-value _-log10_p-value q_statistic q_p-value i2 n_studies n_samples effects +rs12565286 G C -9 -0.008286 0.234417 -0.467743 0.451172 -0.035346 0.971791 0.012427 0.003670 0.998166 0.000000 3 -9 -+- +rs2977670 C G -9 -0.005583 0.234719 -0.465633 0.454467 -0.023785 0.981014 0.008325 0.002566 0.998718 0.000000 3 -9 -+- +rs12138618 G A -9 -0.301597 0.263780 -0.818606 0.215413 -1.143363 0.252868 0.597106 0.743322 0.388599 0.000000 2 -9 --? +rs3094315 G A -9 0.024358 0.059839 -0.092925 0.141642 0.407069 0.683975 0.164960 0.001125 0.999438 0.000000 3 -9 +++ +rs3131968 G A -9 -0.231847 0.096414 -0.420819 -0.042875 -2.404697 0.016207 1.790292 5.384402 0.067732 0.628557 3 -9 --- +rs2519016 T C -9 0.245651 0.211583 -0.169052 0.660354 1.161015 0.245616 0.609744 0.005762 0.997123 0.000000 3 -9 +++ +rs12562034 G A -9 0.009251 0.161478 -0.307246 0.325748 0.057292 0.954295 0.020317 0.000000 1.000000 0.000000 3 -9 +++ +rs12124819 A G -9 0.026341 0.086684 -0.143560 0.196243 0.303875 0.761227 0.118486 0.000001 0.999080 0.000000 2 -9 ++? +rs2980319 T A -9 -0.036137 0.062362 -0.158367 0.086093 -0.579476 0.562290 0.250039 0.034755 0.982773 0.000000 3 -9 --- +rs4040617 A G -9 0.008662 0.058561 -0.106118 0.123443 0.147921 0.882386 0.054341 0.434761 0.804624 0.000000 3 -9 ++- +rs11804171 T A -9 -0.002144 0.287772 -0.566177 0.561889 -0.007450 0.994052 0.002591 0.002162 0.962916 0.000000 2 -9 ?+- +rs2905035 G A -9 -0.044114 0.071935 -0.185107 0.096880 -0.613241 0.539737 0.267817 0.001595 0.968147 0.000000 2 -9 ?-- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gwama.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
