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Tanushree Tunstall bdbc97c40a fix many plot functions to stop them using the "g=ggplot()" pattern, 
which annoyingly throws away lots of useful data that RShiny needs for
clickable plots. Also split the "flame bar" for ligand distance out into
separate functions in generate_distance_colour_map.R. This can now be
easily incorporated into any "wide" graph showing all positions.
2022-08-03 18:58:27 +01:00
config saving changes 2022-02-14 11:14:40 +00:00
dynamut added untracked files in scripts and dynamut 2022-01-04 12:26:54 +00:00
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 Merge branch 'embb_dev' 2021-11-19 08:05:46 +00:00
mcsm_na handled rpob 5uhc position offset in mcsm_ppi2 2022-01-04 10:45:29 +00:00
mcsm_ppi2 handled rpob 5uhc position offset in mcsm_ppi2 2022-01-04 10:45:29 +00:00
scripts fix many plot functions to stop them using the "g=ggplot()" pattern, 2022-08-03 18:58:27 +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
running_scripts added running_scripts to keep track 2022-06-24 15:41:27 +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.