diff interprophet_wrapper.sh @ 9:c04896f31ff7

Added bash wrapper scripts and protxml to table

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet_wrapper.sh	Mon Jun 10 04:58:03 2013 -0500
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+#
+
+# Hard-Coded argument order
+# Args 0-4 are like (eg --no-nss)
+# Args 5 and 6 are like (eg --minprob 0.5)
+# Remaining args are filenames
+#
+actual_output_path_string=$1;shift
+for i in {0 1 2 3 4}; do
+	if [ $1 != "blank" ]; then cmd_args[$i]=$1; fi;shift
+done	
+cmd_args+=($1);shift
+cmd_args+=($1);shift
+
+wd=`pwd`
+
+for original_input_file in $@; do
+	input_file_name=`basename $original_input_file`
+	actual_input_path_string=$wd/$input_file_name.pep.xml
+	ln -s $original_input_file $actual_input_path_string
+	cmd_args+=($actual_input_path_string)
+done
+
+rvm 1.9.3@protk-1.2.2 do interprophet.rb ${cmd_args[@]} -o interprophet_output.pep.xml -r;
+
+if [ -f interprophet_output.pep.xml ]; then
+	for original_input_file in $@; do
+		actual_input_path_string=$wd/`basename $original_input_file`.pep.xml
+		sed -i.bak s%$actual_input_path_string%$original_input_file%g interprophet_output.pep.xml
+	done
+fi
+