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.