adding default dirs and filenames to argparse in foldx and mcsm

mcsm/mcsm.py

@@ -373,7 +373,7 @@ def format_mcsm_output(mcsm_outputcsv):
             
 #%%=====================================================================
     #############
-    # adding column: wild_position
+    # adding column: wild_pos
     # useful for plots and db
     #############
     print('Creating column: wild_pos')

mcsm/mcsm_wrapper.py

@@ -17,7 +17,7 @@ arg_parser.add_argument('-U', '--url',     help='mCSM Server URL', default = 'ht
 arg_parser.add_argument('-c', '--chain',   help='Chain ID as per PDB, Case sensitive', default = 'A')
 arg_parser.add_argument('-l','--ligand',   help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage')
 arg_parser.add_argument('-a','--affinity', help='Affinity in nM', default = 0.99) 
-#arg_parser.add_argument('-p','--pdb_file', help = 'PDB File') 
+arg_parser.add_argument('-pdb','--pdb_file', help = 'PDB File') 
 arg_parser.add_argument('--datadir', help = 'Data Directory')
 arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode')
 
@@ -29,8 +29,8 @@ stage    = args.stage
 chain    = args.chain
 ligand   = args.ligand
 affinity = args.affinity
-#pdb_file = args.pdb_file
-datadir = args.datadir
+pdb_filename = args.pdb_file
+data_dir = args.data_dir
 DEBUG    = args.debug
 
 # Actual Globals :-)
@@ -48,19 +48,21 @@ homedir = os.path.expanduser('~')
 #os.chdir(homedir + '/git/LSHTM_analysis/mcsm')
 gene_match = gene + '_p.'
 
-if datadir:
-    basedir = datadir
+if data_dir:
+    datadir = data_dir
 else:
-    basedir = homedir + '/git/Data'
+    datadir = homedir + '/git/Data'
 
-indir = basedir + '/' + drug + '/' + 'input'
-outdir = basedir + '/' + drug + '/' + 'output'
+indir = datadir + '/' + drug + '/' + 'input'
+outdir = datadir + '/' + drug + '/' + 'output'
 
-in_filename_pdb = gene.lower() + '_complex.pdb'
+if pdb_filename:
+    in_filename_pdb = pdb_filename
+else:
+    in_filename_pdb = gene.lower() + '_complex.pdb'
+    
 infile_pdb = indir + '/' + in_filename_pdb
 
-
-#in_filename_snps = gene.lower() + '_mcsm_snps_test.csv'
 in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile_mcsm_snps, from data_extraction.py)
 infile_snps = outdir + '/' + in_filename_snps
 
@@ -83,11 +85,10 @@ if DEBUG:
     print('DEBUG: formatted CSV output:', outfile_format)
 #%%=====================================================================
 def submit_mcsm():
-
-# Example:
-#    chain = 'A'
-#    ligand_id = 'RMP'
-#    affinity = 10    
+#   Example:
+#   chain = 'A'
+#   ligand_id = 'RMP'
+#   affinity = 10    
 
     print('Result urls and error file (if any) will be written in: ', outdir)