76 lines
2.5 KiB
Text
76 lines
2.5 KiB
Text
#========
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# data extraction: Must be run first to extract mutations for each drug-gene combination
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#========
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./data_extraction.py -d <drug> -g <gene> --make_dirs
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#========
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# add chains to a PDB file: for modeller models lack chain ID, this script is used
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#========
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add_chains_pdb.py <N> MY_PDB.pdb
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#========
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# pdb data extraction: To find out discontinuity of chain and removing invalid muts to allow foldx and mcsm to run properly!
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#========
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In progress...
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#========
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# foldx: specify chain if default is NOT 'A'
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#========
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./runFoldx.py -d <drug> -g <gene> -c1 A -p /media/tanu/eb1d072a-3f73-427f-aeb8-f6852b5c5216/Data/processing
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#========
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# mcsm: specify chain if default is NOT 'A'
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#========
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./run_mcsm.py -d <drug> -g <gene> -s submit -l PZA --debug
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./run_mcsm.py -d <drug> -g <gene> pncA -s get
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./run_mcsm.py -d <drug> -g <gene> pncA -s format
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#====================
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# other struct params
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#====================
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./dssp_df.py -d <drug> -g <gene>
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# Errors on matplot.lib warn=, so just comment it out for the timebeing!: MONKEY PATCH
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./kd_df.py -d <drug> -g <gene> -fasta # fixme: NO of cols says 2, but is actually 3
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./rd_df.py -d <drug> -g <gene> # fixme: input tsv file is sourced manually from website!
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#==============================
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# af_or_calcs.R: calculates af and or
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# opt defaults, uses sensible defaults
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# modified as funciton and checked!
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#==============================
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./af_or_calcs.R -d <drug> -g <gene>
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#==============================
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# af_or calcs: kinship
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#==============================
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#FIXME: configure preformattinga and linking scripts to be generic
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/home/tanu/git/Misc/jody_pza/
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USE THE BELOW from within the or_kinship_link.py script or something?! as part of resolving this!
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/home/tanu/git/LSHTM_analysis/scripts_old/nssnp_info_format.py
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# for now use the file already created using some manual wrestling to link
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# the OR for kinship with mutations
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./or_kinship_link.py -d <drug> -g <gene> -sc <start_coord> -ec <end_coord>
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#==============================
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# formatting: ns<gene>_snp_info.txt
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#==============================
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# This adds mcsm style muts
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./snpinfo_format.py -d <drug> -g <gene>
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#==============================
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# combining dfs: combining_dfs.py
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#==============================
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# FIXME: combining_FIXME.py
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./combining_dfs.py -d <drug> -g <gene>
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#==============================
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mut_electrostatic_changes.py
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# input now mcsm data, maps
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# aa prop and then calculates
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# checked
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# TO DO: could turn to a function
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#==============================
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./mut_electrostatic_changes.py -d <drug> -g <gene>
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