#========
# data extraction: Must be run first to extract mutations for each drug-gene combination
#========
./data_extraction.py -d <drug> -g <gene> --make_dirs

#========
# add chains to a PDB file: for modeller models lack chain ID, this script is used
#========
add_chains_pdb.py <N> MY_PDB.pdb 

#========
# pdb data extraction: To find out discontinuity of chain and removing invalid muts to allow foldx and mcsm to run properly!
#========
In progress...

#========
# foldx: specify chain if default is NOT 'A'
#========
./runFoldx.py -d <drug> -g <gene> -c1 A -p /media/tanu/eb1d072a-3f73-427f-aeb8-f6852b5c5216/Data/processing

#========
# mcsm: specify chain if default is NOT 'A'
#========
./run_mcsm.py -d <drug> -g <gene> -s submit -l PZA --debug
./run_mcsm.py -d <drug> -g <gene> pncA -s get
./run_mcsm.py -d <drug> -g <gene> pncA -s format

#====================
# other struct params
#====================
./dssp_df.py -d <drug> -g <gene>
# Errors on matplot.lib warn=, so just comment it out for the timebeing!: MONKEY PATCH
./kd_df.py -d <drug> -g <gene>  -fasta # fixme: NO of cols says 2, but is actually 3
./rd_df.py -d <drug> -g <gene> # fixme: input tsv file is sourced manually from website!

#==============================
# af_or_calcs.R: calculates af and or
# opt defaults, uses sensible defaults
# modified as funciton and checked!
#==============================
./af_or_calcs.R -d <drug> -g <gene> 

#==============================
# af_or calcs: kinship
#==============================
#FIXME: configure preformattinga and linking scripts to be generic
/home/tanu/git/Misc/jody_pza/

USE THE BELOW from within the or_kinship_link.py script or something?! as part of resolving this!
/home/tanu/git/LSHTM_analysis/scripts_old/nssnp_info_format.py

# for now use the file already created using some manual wrestling to link
# the OR for kinship with mutations

./or_kinship_link.py -d <drug> -g <gene> -sc <start_coord> -ec <end_coord>

#==============================
# formatting: ns<gene>_snp_info.txt
#==============================
# This adds mcsm style muts
./snpinfo_format.py -d <drug> -g <gene>

#==============================
# combining dfs: combining_dfs.py
#==============================
# FIXME: combining_FIXME.py
./combining_dfs.py -d <drug> -g <gene>

#==============================
mut_electrostatic_changes.py
# input now mcsm data, maps 
# aa prop and then calculates
# checked
# TO DO: could turn to a function
#==============================
./mut_electrostatic_changes.py -d <drug> -g <gene>
