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README.md

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+mCSM Analysis
+=============
+
+This repo does mCSM analysis using Python (Pandas, numpy), bash and R.
+
+Requires an additional 'Data' directory (Supplied separately). Batteries not included.
+
+ # directory struc
+
+ # Assumptions
+
+ 1. git repos are cloned to `~/git`
+ 2. The script
+
+## LSHTM\_analysis: Repo
+
+ subdirs
+
+ needs to call `../Data/input/original/`
+
+ meta\_data\_analysis/
+ 	*.R
+ 	*.py
+	
+ needs to call `../Data/input/processed/<drug>`
+ needs to output `../Data/output/results/<drug>`
+
+ mcsm\_analysis/
+	<drug>/ (generated by `meta_data_analysis/pnca_data_extraction.py`. To be replaced with command line args or config option "soon")
+		scripts/ (changed from `Scripts/`)
+		*.R
+		*.py
+			mcsm/
+			*.sh
+			*.py
+			*.R
+			plotting/
+			*.R
+
+
+Data: Repo:
+
+ # subdirs
+
+	input/
+		original/
+		processed/
+	
+	output/
+	    <drug>/ (generated by `meta_data_analysis/pnca_data_extraction.py`. To be replaced with command line args or config option "soon")
+    		results/
+        		*.csv
+        		*.xlsx
+        		*.doc
+        		*.txt
+                plots/
+                structure/
+
+More docs here as I write them.