From d6552628e4515ba87bd048fdec2346e21fa079f2 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 26 Aug 2020 17:20:01 +0100 Subject: [PATCH] added running scripts doc --- scripts/running_scripts | 51 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 scripts/running_scripts diff --git a/scripts/running_scripts b/scripts/running_scripts new file mode 100644 index 0000000..9889ec8 --- /dev/null +++ b/scripts/running_scripts @@ -0,0 +1,51 @@ +#======== +# 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 + +