updated readme

README.md

@@ -1,33 +1,26 @@
 mCSM Analysis
 =============
 
-This repo does mCSM analysis using Python (Pandas, numpy), bash and R.
+This repo does mCSM analysis using Python, bash and R.
 
-Requires an additional 'Data' directory (Supplied separately). Batteries not included.
+Requires an additional 'Data' directory. Batteries not included.
 
- # directory struc
-
- # Assumptions
+    # Assumptions
 
  1. git repos are cloned to `~/git`
- 2. The script
+ 2. Requires a `Data/` in `~/git` which has the struc created by `mk-drug-dirs.sh` 
 
-## LSHTM\_analysis: Repo
+## LSHTM\_analysis: 
  
  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/`)
+		scripts/
 		*.R
 		*.py
 			mcsm/
@@ -37,23 +30,4 @@ Requires an additional 'Data' directory (Supplied separately). Batteries not inc
 			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.

mk-drug-dirs.sh

@@ -1,8 +1,7 @@
 #!/bin/bash
 # Create a drug directory structure for processing
 #
-#
-# Structure:
+## Structure:
 #
 # $DATA_DIR/$DRUG/input
 #                 |- original