[Genabel-commits] r1195 - in pkg/ProbABEL/tests: . verified_results

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

Author: lckarssen
Date: 2013-04-17 10:10:42 +0200 (Wed, 17 Apr 2013)
New Revision: 1195

Modified:
   pkg/ProbABEL/tests/check_dose_input.sh
   pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
   pkg/ProbABEL/tests/verified_results/height_add.out.txt
   pkg/ProbABEL/tests/verified_results/height_base_add.out.txt
Log:
ProbABEL tests:
- scripts: send screen output to /dev/null for less cluttered screen
- verified results: update to the fact that the dose file is now based on the prob file (see SVN r1093).



Modified: pkg/ProbABEL/tests/check_dose_input.sh
===================================================================
--- pkg/ProbABEL/tests/check_dose_input.sh	2013-04-17 08:07:05 UTC (rev 1194)
+++ pkg/ProbABEL/tests/check_dose_input.sh	2013-04-17 08:10:42 UTC (rev 1195)
@@ -22,7 +22,7 @@
     -i ${exampledir}/test.mlinfo \
     -m ${exampledir}/test.map \
     -c 19 \
-    -o height_base
+    -o height_base > /dev/null
 
 echo -n "  Verifying $outfile: "
 if diff $outfile $results/$outfile; then

Modified: pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
===================================================================
--- pkg/ProbABEL/tests/check_probabel.pl_chunk.sh	2013-04-17 08:07:05 UTC (rev 1194)
+++ pkg/ProbABEL/tests/check_probabel.pl_chunk.sh	2013-04-17 08:10:42 UTC (rev 1195)
@@ -108,7 +108,7 @@
     outfile="height_add.out.txt"
 
     echo "Checking output using dosages $WithOrWithout chunks..."
-    ./probabel.pl 1 2 linear $1 --additive height
+    ./probabel.pl 1 2 linear $1 --additive height > /dev/null
     echo -n "  Verifying $outfile: "
     if diff $outfile $results/$outfile; then
         echo -e "\t\tOK"
@@ -123,7 +123,7 @@
     height_ngp2_add.out.txt"
 
     echo "Checking output using probabilities $WithOrWithout chunks..."
-    ./probabel.pl 1 2 linear $1 --allmodels height -o _ngp2
+    ./probabel.pl 1 2 linear $1 --allmodels height -o _ngp2 > /dev/null
     for file in $outfilelist; do
         echo -n "  Verifying $file: "
         if diff $file $results/$file; then

Modified: pkg/ProbABEL/tests/verified_results/height_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_add.out.txt	2013-04-17 08:07:05 UTC (rev 1194)
+++ pkg/ProbABEL/tests/verified_results/height_add.out.txt	2013-04-17 08:10:42 UTC (rev 1195)
@@ -1,6 +1,6 @@
 name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.56444 1 204938 -0.218693 0.734966 -428.971
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 182 0.564412 1 207859 -0.218352 0.734214 -428.971
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 181 0.498997 2 211970 0.280289 0.728449 -427.081
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.561132 2 212033 -0.216918 0.7259 -428.971
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.929684 2 217034 2.23335 1.30142 -427.523
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3847112 76.6301612 -428.98
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -25.763226 86.4877202 -426.965
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -40.7722369 102.559115 -428.936
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 35.3601998 81.7868565 -428.921
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 -112.234833 141.168963 -428.694

Modified: pkg/ProbABEL/tests/verified_results/height_base_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_base_add.out.txt	2013-04-17 08:07:05 UTC (rev 1194)
+++ pkg/ProbABEL/tests/verified_results/height_base_add.out.txt	2013-04-17 08:10:42 UTC (rev 1195)
@@ -1,6 +1,6 @@
 name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.56444 19 204938 -0.218693 0.734966 -428.971
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 182 0.564412 19 207859 -0.218352 0.734214 -428.971
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 181 0.498997 19 211970 0.280289 0.728449 -427.081
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.561132 19 212033 -0.216918 0.7259 -428.971
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.929684 19 217034 2.23335 1.30142 -427.523
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 19 204938 20.3847112 76.6301612 -428.98
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 19 207859 -25.763226 86.4877202 -426.965
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 19 211970 -40.7722369 102.559115 -428.936
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 19 212033 35.3601998 81.7868565 -428.921
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 19 217034 -112.234833 141.168963 -428.694