fixed white space prob with mcsm input with merge

mcsm/run_mcsm.py

@@ -18,29 +18,39 @@ arg_parser.add_argument('-c', '--chain',   help='Chain ID as per PDB, Case sensi
 arg_parser.add_argument('-l','--ligand',   help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage', default = None)
 arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 0.99) 
 arg_parser.add_argument('-pdb','--pdb_file', help = 'PDB File') 
-arg_parser.add_argument('--datadir', help = 'Data Directory')
+
+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('--debug', action='store_true', help = 'Debug Mode')
 
 args = arg_parser.parse_args()
-
-gene     = args.gene
-drug     = args.drug
-stage    = args.stage
-chain    = args.chain
-ligand   = args.ligand
-affinity = args.affinity
-pdb_filename = args.pdb_file
-data_dir = args.data_dir
-DEBUG    = args.debug
-
-# Actual Globals :-)
-host = args.host
-prediction_url = args.url
-
+#=======================================================================
+#%% variables
 #host = "http://biosig.unimelb.edu.au"
 #prediction_url = f"{host}/mcsm_lig/prediction"
 #drug = 'isoniazid'
 #gene = 'KatG'
+#%%=====================================================================
+# Command line options
+gene         = args.gene
+drug         = args.drug
+stage        = args.stage
+chain        = args.chain
+ligand       = args.ligand
+affinity     = args.affinity
+pdb_filename = args.pdb_file
+
+datadir      = args.datadir
+indir        = args.input_dir
+outdir       = args.output_dir
+
+DEBUG        = args.debug
+
+# Actual Globals :-)
+host = args.host
+prediction_url = args.url
 
 # submit_mcsm globals
 homedir = os.path.expanduser('~')
@@ -51,13 +61,14 @@ gene_match = gene + '_p.'
 #============
 # directories
 #============
-if data_dir:
-    datadir = data_dir
-else:
-    datadir = homedir + '/git/Data'
-
-indir = datadir + '/' + drug + '/' + 'input'
-outdir = datadir + '/' + drug + '/' + 'output'
+if not datadir:
+    datadir = homedir + '/' + 'git/Data'
+    
+if not indir:
+    indir = datadir + '/' + drug + '/input'
+    
+if not outdir:
+    outdir = datadir + '/' + drug + '/output'
 
 #=======
 # input