WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / Kinfold / Laplace / laplace.sh

diff --git a/binaries/src/ViennaRNA/Kinfold/Laplace/laplace.sh b/binaries/src/ViennaRNA/Kinfold/Laplace/laplace.sh
new file mode 100644 (file)
index 0000000..73b32ce
--- /dev/null
+++ b/binaries/src/ViennaRNA/Kinfold/Laplace/laplace.sh
@@ -0,0 +1,26 @@
+#!/bin/sh
+
+# strip leading path and tailing extension(s)
+function to_basename {
+    local basename=${1%/}
+    basename=${basename##*/}
+    basename=${basename%%.*}
+    echo $basename
+}
+
+KINFOLD=../Kinfold
+INFILE=$1
+
+OUTFILE=$(to_basename $INFILE)
+
+for phi in `seq 0.3 0.1 8.0`
+do
+ $KINFOLD \
+ --silent --phi $phi --log $OUTFILE.$phi --num 2000 --time 1000000 < $INFILE
+done
+
+perl extract_data.pl *.log > $OUTFILE.data
+
+R CMD BATCH to_boxplot.R
+
+# End of file