#======== # foldx #======== ./runFoldx.py -d pyrazinamide -g pncA #======== # mcsm #======== ./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA ./run_mcsm.py -d pyrazinamide -g pncA -s get ./run_mcsm.py -d pyrazinamide -g pncA -s format #==================== # other struct params #==================== ./dssp_df.py -d pyrazinamide -g pncA ./kd_df.py -d pyrazinamide -g pncA # fixme: NO of cols says 2,but is actually 3 ./rd_df.py -d pyrazinamide -g pncA # fixme: input tsv file is sourced manually from website! #============================== # af_or calcs: different types #============================== ./af_or_calcs.R --d pyrazinamide --gene pncA # fixme: No conditional dir structure #============================== # 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 pyrazinamide -g pncA -sc 2288681 -ec 2289241 #============================== # formatting: ns_snp_info.txt #============================== # This adds mcsm style muts ./snpinfo_format.py -d pyrazinamide -g pncA #============================== # combining dfs: combining_dfs.py #============================== # FIXME: combining_FIXME.py ./combining_dfs.py -d pyrazinamide -g pncA