tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity
Code to be made public
381 commits 3 branches 0 tags 40 MiB
Find a file
Tanushree Tunstall b12a7769ca updated .gitignore
2021-02-18 12:01:04 +00:00
dynamut add files 2021-02-18 11:50:46 +00:00
foldx added sample test_snps 2021-02-10 10:38:08 +00:00
mcsm uncommented some debug output for mcsm, pandas and numpy conflict. So temporarily resolved it by running from base env 2021-02-11 10:53:23 +00:00
mcsm_na renamed file in mcsm_na to be consistent 2021-02-18 10:51:17 +00:00
scripts dynamut scripts and minor change dir for rd_df.py 2021-02-10 15:40:33 +00:00
.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 added R header file to base dir to allow general access by R scripts 2020-03-28 17:56:39 +00:00
README.md Update README.md 2020-09-21 18:11:24 +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.