tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity
Code to be made public
957 commits 3 branches 0 tags 40 MiB
Find a file
Tanushree Tunstall e9fb582db9 msa indexes
2022-09-05 18:49:40 +01:00
config added 113 to alr aa 2022-09-04 21:36:14 +01:00
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 msa indexes 2022-09-05 18:49:40 +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 various usability tweaks to LogoPlotMSA and position_annotation 2022-09-05 16:06:10 +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.