56 lines
1.7 KiB
Text
56 lines
1.7 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 pyrazinamide -g pncA
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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 pyrazinamide -g pncA
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#========
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# mcsm
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#========
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./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA
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./run_mcsm.py -d pyrazinamide -g pncA -s get
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./run_mcsm.py -d pyrazinamide -g 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 pyrazinamide -g pncA
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./kd_df.py -d pyrazinamide -g pncA # fixme: NO of cols says 2,but is actually 3
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./rd_df.py -d pyrazinamide -g pncA # fixme: input tsv file is sourced manually from website!
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#==============================
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# af_or calcs: different types
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#==============================
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./af_or_calcs.R --d pyrazinamide --gene pncA # fixme: No conditional dir structure
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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 pyrazinamide -g pncA -sc 2288681 -ec 2289241
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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 pyrazinamide -g pncA
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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 pyrazinamide -g pncA
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