refactoring code to make it take command line args

README.md

@@ -1,8 +1,10 @@
 mCSM Analysis
 =============
 
-This repo does mCSM analysis using bash, python and R.
-
+This contains scripts that does the following:
+ 1. mCSM analysis: using bash, python and R
+ 2. meta data analysis: using python and R
+ 
 Requires an additional 'Data' directory. Batteries not included:-)
 
 ## Assumptions
@@ -19,17 +21,14 @@ subdirs within this repo
  	*.R
  	*.py
 	
- mcsm\_analysis/
-	<drug>/
-		scripts/
-		*.R
-		*.py
-			mcsm/
-			*.sh
-			*.py
-			*.R
-			plotting/
-			*.R
+ mcsm_analysis
+#	<drug>/
+
+ foldx_analysis
+ 
+ plotting
+ 	*.R
+ 
 ```
 
 More docs here as I write them.