[Genabel-commits] r1224 - branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-05-19 16:52:04 +0200 (Sun, 19 May 2013)
New Revision: 1224

Modified:
   branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/Makefile.am
   branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_bt.sh
   branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_mms.sh
   branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_qt.sh
   branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/test.mlinfo
Log:
In ProbABEL coxfix 0.3.0 branch: updated examples to latest versions from trunk (r1223)



Modified: branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/Makefile.am
===================================================================
--- branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/Makefile.am	2013-05-17 07:27:46 UTC (rev 1223)
+++ branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/Makefile.am	2013-05-19 14:52:04 UTC (rev 1224)
@@ -4,7 +4,8 @@
 
 examplefiles = height_ngp2_robust_int1_over_domin.out.txt.save		\
  test.prob.fvi mmscore_gen.prob.fvd test.map mldose.IDS			\
- impute_with_missing.mlinfo  height_ngp2_robust_int1_recess.out.txt.save \
+ impute_with_missing.mlinfo run_diff.sh					\
+ height_ngp2_robust_int1_recess.out.txt.save				\
  height_ngp2_2df.out.txt.save mmscore_gen.mlprob mmscore_gen.mlinfo	\
  height_ngp2_robust_recess.out.txt.save example_cox.sh test.mlprob	\
  test.prob.fvd impute_with_missing_robust_int1_add.out.txt.save		\
@@ -43,7 +44,7 @@
 exampledir = $(pkgdatadir)/examples
 dist_example_DATA = $(examplefiles)
 
-TESTS_ENVIRONMENT = sh
+TESTS_ENVIRONMENT = bash
 check_SCRIPTS = example_bt.sh example_qt.sh example_mms.sh
 if BUILD_pacoxph
 check_SCRIPTS +=  example_cox.sh

Modified: branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_bt.sh
===================================================================
--- branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_bt.sh	2013-05-17 07:27:46 UTC (rev 1223)
+++ branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_bt.sh	2013-05-19 14:52:04 UTC (rev 1224)
@@ -2,13 +2,13 @@
 # This script runs checks on ProbABEL's palogist module for
 # binary traits.
 
-. ./run_diff.sh
-
 echo "analysing BT"
 if [ -z ${srcdir} ]; then
     srcdir="."
 fi
 
+. ${srcdir}/run_diff.sh
+
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
 exec 3>/dev/null

Modified: branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_mms.sh
===================================================================
--- branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_mms.sh	2013-05-17 07:27:46 UTC (rev 1223)
+++ branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_mms.sh	2013-05-19 14:52:04 UTC (rev 1224)
@@ -2,13 +2,13 @@
 # This script runs checks on ProbABEL's palinear module for
 # quantitative traits combined with the mmscore option.
 
-. ./run_diff.sh
-
 echo "analysis using MMScore"
 if [ -z ${srcdir} ]; then
     srcdir="."
 fi
 
+. ${srcdir}/run_diff.sh
+
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
 exec 3>/dev/null
@@ -35,8 +35,8 @@
     >& 3
 
 
-run_diff mmscore_dose_add.out.txt \
-    mmscore_dose_fv_add.out.txt \
+run_diff mmscore_add.out.txt \
+    mmscore_fv_add.out.txt \
     "mmscore check: dose vs. dose_fv"
 
 

Modified: branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_qt.sh
===================================================================
--- branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_qt.sh	2013-05-17 07:27:46 UTC (rev 1223)
+++ branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/example_qt.sh	2013-05-19 14:52:04 UTC (rev 1224)
@@ -2,13 +2,14 @@
 # This script runs checks on ProbABEL's palinear module for
 # quantitative traits.
 
-. ./run_diff.sh
-
 echo "analysing QT"
 if [ -z ${srcdir} ]; then
     srcdir="."
 fi
 
+. ${srcdir}/run_diff.sh
+
+
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
 exec 3>/dev/null

Modified: branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/test.mlinfo
===================================================================
--- branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/test.mlinfo	2013-05-17 07:27:46 UTC (rev 1223)
+++ branches/ProbABEL-pacox/v.0.3.0/ProbABEL/examples/test.mlinfo	2013-05-19 14:52:04 UTC (rev 1224)
@@ -1,6 +1,6 @@
 SNP	Al1	Al2	Freq1	MAF	Quality	Rsq
-rs7247199	G	A	0.5847	0.4150	0.9299	0.8666
-rs8102643	C	T	0.5847	0.4150	0.9308	0.8685
+rs7247199	GAC	A	0.5847	0.4150	0.9299	0.8666
+rs8102643	C	TGGT	0.5847	0.4150	0.9308	0.8685
 rs8102615	T	A	0.5006	0.4702	0.9375	0.8932
 rs8105536	G	A	0.5783	0.4213	0.9353	0.8832
 rs2312724	T	C	0.9122	0.0877	0.9841	0.9232