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cherry-pick mcsm_na/run_format_results_mcsm_na.py from master to ensure consistency

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Tanushree Tunstall 2021-10-28 12:54:04 +01:00
parent 7d6087c82e
commit 80f73a3697
1 changed files with 37 additions and 8 deletions
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45
mcsm_na/run_format_results_mcsm_na.py
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@ -11,16 +11,45 @@ homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
from format_results_mcsm_na import *
########################################################################
# variables
#%% command line args
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('-d', '--drug' , help = 'drug name (case sensitive)', default = None)
arg_parser.add_argument('-g', '--gene' , help = 'gene name (case sensitive)', default = None)
arg_parser.add_argument('--datadir' , help = 'Data Directory. By default, it assmumes homedir + git/Data')
arg_parser.add_argument('-i', '--input_dir' , help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
#arg_parser.add_argument('--mkdir_name' , help = 'Output dir for processed results. This will be created if it does not exist')
arg_parser.add_argument('-m', '--make_dirs' , help = 'Make dir for input and output', action='store_true')
# TODO: add cmd line args
arg_parser.add_argument('--debug' , action = 'store_true' , help = 'Debug Mode')
gene = 'gid'
drug = 'streptomycin'
datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input'
outdir = datadir + '/' + drug + '/output'
outdir_na = outdir + '/mcsm_na_results/'
args = arg_parser.parse_args()
#%%============================================================================
# variable assignment: input and output paths & filenames
drug = args.drug
gene = args.gene
datadir = args.datadir
indir = args.input_dir
outdir = args.output_dir
#outdir_ppi2 = args.mkdir_name
make_dirs = args.make_dirs
#=======
# dirs
#=======
if not datadir:
datadir = homedir + '/git/Data/'
if not indir:
indir = datadir + drug + '/input/'
if not outdir:
outdir = datadir + drug + '/output/'
#if not mkdir_name:
# outdir_na = outdir + 'mcsm_na_results/'
outdir_na = outdir + 'mcsm_na_results/'
# Input file
infile_mcsm_na = outdir_na + gene + '_output_combined_clean.tsv'