Mercurial > repos > iracooke > tpp_prophets

diff protein_prophet_wrapper.sh @ 9:c04896f31ff7

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Added bash wrapper scripts and protxml to table
author Ira Cooke <iracooke@gmail.com>
date Mon, 10 Jun 2013 04:58:03 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_prophet_wrapper.sh	Mon Jun 10 04:58:03 2013 -0500
@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+#
+
+actual_output_path_string=$1;shift
+original_input_file=$1;shift
+
+# Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input 
+# name because peptide prophet can't handle anything else
+
+wd=`pwd`
+
+actual_input_path_string=$wd/`basename $original_input_file`.pep.xml
+
+ln -s $original_input_file $actual_input_path_string
+
+rvm 1.9.3@protk-1.2.2 do protein_prophet.rb $actual_input_path_string $@ -o protein_prophet_results.prot.xml
+
+if [ -f protein_prophet_results.prot.xml ]; then
+	sed -i.bak s%$actual_input_path_string%$original_input_file.pep.xml%g protein_prophet_results.prot.xml
+fi
+