[med-svn] [gwama] 01/03: Added tests
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Fri Dec 19 07:43:51 UTC 2014
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository gwama.
commit c8563e48d23f4545fdf954c50096347761f533dd
Author: Dylan Aïssi <bob.dybian at gmail.com>
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 <debian-med-packaging at lists.alioth.debian.
Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
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 <bob.dybian at gmail.com>
+# 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 ?--
--
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