tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

updating notes to running_scripts.py as running for another drug-target

Browse source
This commit is contained in:
Tanushree Tunstall 2020-11-17 13:55:16 +00:00
parent d4cd5aea0a
commit 2911678177
3 changed files with 6 additions and 4 deletions
Download patch file Download diff file Expand all files Collapse all files

2
foldx/runFoldx.py
View file

@ -82,7 +82,7 @@ if not outdir:
# FIXME: this is a temporary directory and should be correctly handled # FIXME: this is a temporary directory and should be correctly handled
process_dir = datadir + '/' + drug +'/' + 'processing' process_dir = datadir + '/' + drug +'/' + 'processing'
os.mkdir(process_dir) #os.mkdir(process_dir)
#======= #=======
# input # input
#======= #=======

1
scripts/dssp_df.py
View file

@ -156,6 +156,7 @@ def extract_chain_dssp(inputpdbfile):
return pdbchainlist return pdbchainlist
#======================================================================= #=======================================================================
#%% write csv of processed dssp output #%% write csv of processed dssp output
# FIXME specify chain as cmd option!
def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']): def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']):
""" """
Create a df from a dssp file containing ASA, RSA, SS for all chains Create a df from a dssp file containing ASA, RSA, SS for all chains

7
scripts/running_scripts
View file

@ -9,9 +9,9 @@
./runFoldx.py -d pyrazinamide -g pncA ./runFoldx.py -d pyrazinamide -g pncA
#======== #========
# mcsm # mcsm: specify chain if default is NOT 'A'
#======== #========
./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA ./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 get
./run_mcsm.py -d pyrazinamide -g pncA -s format ./run_mcsm.py -d pyrazinamide -g pncA -s format
@ -19,7 +19,8 @@
# other struct params # other struct params
#==================== #====================
./dssp_df.py -d pyrazinamide -g pncA ./dssp_df.py -d pyrazinamide -g pncA
./kd_df.py -d pyrazinamide -g pncA # fixme: NO of cols says 2,but is actually 3 # 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! ./rd_df.py -d pyrazinamide -g pncA # fixme: input tsv file is sourced manually from website!
#============================== #==============================