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/ / (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.