[Genabel-commits] r1515 - pkg/ProbABEL/checks
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 30 14:33:54 CET 2013
Author: lckarssen
Date: 2013-12-30 14:33:53 +0100 (Mon, 30 Dec 2013)
New Revision: 1515
Modified:
pkg/ProbABEL/checks/test_bt.sh
pkg/ProbABEL/checks/test_cox.sh
pkg/ProbABEL/checks/test_mms.sh
pkg/ProbABEL/checks/test_qt.sh
Log:
In ProbABEL's check scripts:
- make one variable for the location of the binaries
- Added a $scriptdir variable that contains the directory in which the scripts are located. Makes it easier to find the run_diff.sh script shared by all four test scripts.
Modified: pkg/ProbABEL/checks/test_bt.sh
===================================================================
--- pkg/ProbABEL/checks/test_bt.sh 2013-12-29 16:19:49 UTC (rev 1514)
+++ pkg/ProbABEL/checks/test_bt.sh 2013-12-30 13:33:53 UTC (rev 1515)
@@ -3,11 +3,14 @@
# binary traits.
echo "analysing BT"
+
+scriptdir=$(dirname $0)
+
if [ -z ${srcdir} ]; then
srcdir="."
fi
-. ${srcdir}/run_diff.sh
+. ${scriptdir}/run_diff.sh
inputdir=${srcdir}/inputfiles
@@ -18,7 +21,9 @@
exec 3>&1
fi
-../src/palogist \
+palogist=../src/palogist
+
+$palogist \
-p ${inputdir}/logist_data.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
@@ -27,7 +32,7 @@
-o logist \
>& 3
-../src/palogist \
+$palogist \
-p ${inputdir}/logist_data.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -41,7 +46,7 @@
logist_fv_add.out.txt \
"BT check: dose vs. dose_fv"
-../src/palogist \
+$palogist \
-p ${inputdir}/logist_data.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -51,7 +56,7 @@
-o logist_prob \
>& 3
-../src/palogist \
+$palogist \
-p ${inputdir}/logist_data.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
Modified: pkg/ProbABEL/checks/test_cox.sh
===================================================================
--- pkg/ProbABEL/checks/test_cox.sh 2013-12-29 16:19:49 UTC (rev 1514)
+++ pkg/ProbABEL/checks/test_cox.sh 2013-12-30 13:33:53 UTC (rev 1515)
@@ -2,11 +2,14 @@
# This script runs checks on ProbABEL's pacoxph module
echo "Analysing Cox model..."
+
+scriptdir=$(dirname $0)
+
if [ -z ${srcdir} ]; then
srcdir="."
fi
-. ${srcdir}/run_diff.sh
+. ${scriptdir}/run_diff.sh
inputdir=${srcdir}/inputfiles
@@ -18,7 +21,9 @@
exec 3>&1
fi
-../src/pacoxph \
+pacoxph=../src/pacoxph
+
+$pacoxph \
-p ${inputdir}/coxph_data.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
@@ -27,7 +32,7 @@
-o coxph_dose \
>& 3
-../src/pacoxph \
+$pacoxph \
-p ${inputdir}/coxph_data.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -40,7 +45,7 @@
"pacoxph check: dose vs. dose_fv"
-../src/pacoxph \
+$pacoxph \
-p ${inputdir}/coxph_data.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -54,7 +59,7 @@
"pacoxph check: dose vs. prob" -I SNP
-../src/pacoxph \
+$pacoxph \
-p ${inputdir}/coxph_data.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
Modified: pkg/ProbABEL/checks/test_mms.sh
===================================================================
--- pkg/ProbABEL/checks/test_mms.sh 2013-12-29 16:19:49 UTC (rev 1514)
+++ pkg/ProbABEL/checks/test_mms.sh 2013-12-30 13:33:53 UTC (rev 1515)
@@ -18,7 +18,9 @@
exec 3>&1
fi
-../src/palinear \
+palinear=../src/palinear
+
+$palinear \
-p ${inputdir}/mmscore_pheno.PHE \
-i ${inputdir}/mmscore_gen.mlinfo \
-d ${inputdir}/mmscore_gen.mldose \
@@ -27,7 +29,7 @@
--mmscore ${inputdir}/mmscore_InvSigma_aj.sex.age.dat \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/mmscore_pheno.PHE \
-i ${inputdir}/mmscore_gen.mlinfo \
-d ${inputdir}/mmscore_gen.dose.fvi \
@@ -42,7 +44,7 @@
"mmscore check: dose vs. dose_fv"
-../src/palinear \
+$palinear \
-p ${inputdir}/mmscore_pheno.PHE \
-i ${inputdir}/mmscore_gen.mlinfo \
-d ${inputdir}/mmscore_gen.mlprob \
@@ -51,7 +53,7 @@
--mmscore ${inputdir}/mmscore_InvSigma_aj.sex.age.dat \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/mmscore_pheno.PHE \
-i ${inputdir}/mmscore_gen.mlinfo \
-d ${inputdir}/mmscore_gen.prob.fvi \
Modified: pkg/ProbABEL/checks/test_qt.sh
===================================================================
--- pkg/ProbABEL/checks/test_qt.sh 2013-12-29 16:19:49 UTC (rev 1514)
+++ pkg/ProbABEL/checks/test_qt.sh 2013-12-30 13:33:53 UTC (rev 1515)
@@ -1,13 +1,16 @@
-#!/bin/bash -x
+#!/bin/bash
# This script runs checks on ProbABEL's palinear module for
# quantitative traits.
echo "analysing QT"
+
+scriptdir=$(dirname $0)
+
if [ -z ${srcdir} ]; then
srcdir="."
fi
-. ${srcdir}/run_diff.sh
+. ${scriptdir}/run_diff.sh
inputdir=${srcdir}/inputfiles
@@ -18,8 +21,10 @@
exec 3>&1
fi
+palinear="../src/palinear"
+
echo "base analysis"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
@@ -27,7 +32,7 @@
-c 19 \
-o linear_base \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -43,14 +48,14 @@
echo "Option --allcov"
-../src/palinear -p ${inputdir}/height.txt \
+$palinear -p ${inputdir}/height.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --allcov \
-o linear_allcov \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -65,7 +70,7 @@
echo "Option --interaction=1"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
@@ -73,7 +78,7 @@
-c 19 --interaction=1 \
-o linear_int1 \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -88,7 +93,7 @@
echo "Option --robust"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
@@ -96,7 +101,7 @@
-c 19 --robust \
-o linear_robust \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -111,7 +116,7 @@
echo "Option --robust --interaction=1"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
@@ -119,7 +124,7 @@
-c 19 --robust --interaction=1 \
-o linear_robust_int1 \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
@@ -134,7 +139,7 @@
echo "Option --ngp=2, mlprob file"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -142,7 +147,7 @@
-c 19 --ngp=2 \
-o linear_ngp2 \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
@@ -165,7 +170,7 @@
echo "Option --ngp=2 --allcov"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -173,7 +178,7 @@
-c 19 --ngp=2 --allcov \
-o linear_ngp2_allcov \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
@@ -190,7 +195,7 @@
echo "Option --ngp=2 --interaction=1"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -198,7 +203,7 @@
-c 19 --ngp=2 --interaction=1 \
-o linear_ngp2_int1 \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
@@ -215,7 +220,7 @@
echo "Option --ngp=2 --robust"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -223,7 +228,7 @@
-c 19 --ngp=2 --robust \
-o linear_ngp2_robust \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
@@ -240,7 +245,7 @@
echo "Option --ngp=2 --robust --interaction=1"
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
@@ -248,7 +253,7 @@
-c 19 --ngp=2 --robust --interaction=1 \
-o linear_ngp2_robust_int1 \
>& 3
-../src/palinear \
+$palinear \
-p ${inputdir}/height.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
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