diff --git a/mcsm_na/run_format_results_mcsm_na.py b/mcsm_na/run_format_results_mcsm_na.py
index d990368..a5886b4 100644
--- a/mcsm_na/run_format_results_mcsm_na.py
+++ b/mcsm_na/run_format_results_mcsm_na.py
@@ -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
-# Imagine we've done the work
-gene = 'gid'
-drug = 'streptomycin'
-datadir = homedir + '/git/Data'
-indir = datadir + '/' + drug + '/input'
-outdir = datadir + '/' + drug + '/output'
-outdir_na = outdir + '/mcsm_na_results/'
+arg_parser.add_argument('--debug'           , action = 'store_true' , help = 'Debug Mode')
+
+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'