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Tanushree Tunstall 2021-02-09 16:03:02 +00:00
parent 4d03a43c4a
commit 660ab31ce8
2 changed files with 86 additions and 65 deletions
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scripts/running_scripts
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@ -1,32 +1,42 @@
#========
# data extraction: Must be run first to extract mutations for each drug-gene combination
#========
./data_extraction.py -d pyrazinamide -g pncA
./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 pyrazinamide -g pncA
./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 pyrazinamide -g pncA -s submit -l PZA --debug
./run_mcsm.py -d pyrazinamide -g pncA -s get
./run_mcsm.py -d pyrazinamide -g pncA -s format
./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 pyrazinamide -g pncA
./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 pyrazinamide -g pncA -fasta # 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!
./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: different types
#==============================
./af_or_calcs.R --d pyrazinamide --gene pncA # fixme: No conditional dir structure
./af_or_calcs.R -d <drug> -g <gene># fixme: No conditional dir structure
#==============================
# af_or calcs: kinship
@ -40,18 +50,18 @@ USE THE BELOW from within the or_kinship_link.py script or something?! as part o
# 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
./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 pyrazinamide -g pncA
./snpinfo_format.py -d <drug> -g <gene>
#==============================
# combining dfs: combining_dfs.py
#==============================
# FIXME: combining_FIXME.py
./combining_dfs.py -d pyrazinamide -g pncA
./combining_dfs.py --d <drug> -g <gene>