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Tanushree Tunstall 59337c7b71 pull in merged changes to mcsm_na/run_format_results_mcsm_na.py from master, including the merge fix
2021-10-28 12:48:00 +01:00
config added config/ with drug gene names 2021-09-16 10:05:28 +01:00
dynamut added gene.lower to dynamut2 format result script 2021-10-19 11:12:34 +01:00
foldx fix runFoldx so that it looks for a missing rotabase.txt in the process_dir and also print the foldx command that will be run 2021-09-29 18:24:06 +01:00
mcsm split csv for isoniazid 2021-09-20 16:12:45 +01:00
mcsm_na pull in merged changes to mcsm_na/run_format_results_mcsm_na.py from master, including the merge fix 2021-10-28 12:48:00 +01:00
scripts much development 2021-10-28 10:41:43 +01:00
.gitignore updated .gitignore 2021-02-18 12:01:04 +00:00
LICENCE added licence 2020-01-08 16:51:47 +00:00
mk_drug_dirs.sh refactoring code to make it take command line args 2020-04-06 19:03:41 +01:00
my_header.R split csv for isoniazid 2021-09-20 16:12:45 +01:00
README.md test branch commit 2021-06-04 09:43:48 +01:00

README.md

mCSM

This contains scripts that does the following:

  1. mcsm.py: function for submitting mcsm job and extracting results
  2. run_mcsm.py: wrapper to call mcsm.py

foldx

This contains scripts that does the following:

  1. runFoldx.py: submitting foldx requests and extracting results
  2. runfoldx.sh: is wrapped by runFoldx.py

Requires an additional 'Data' directory. Batteries not included:-)

Assumptions

  1. git repos are cloned to ~/git
  2. Requires a data directory with an input and output subdirs. Can be specified on the CLI with --datadir, and optionally can be created with mk_drug_dirs.sh <DRUG_NAME>

LSHTM_analysis:

subdirs within this repo

 scripts
 	*.R
 	*.py
	plotting/
	*.R
 mcsm
	*.py
 foldx
 	*.py
	*.sh

More docs here as I write them.