add foldx5 wrapper

foldx/runFoldx.py

@@ -40,7 +40,7 @@ arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb fi
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
 arg_parser.add_argument('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + <drug> + processing. Make sure it is somewhere with LOTS of storage as it writes all output!') #FIXME
 
-arg_parser.add_argument('-pdb', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb in input_dir')
+arg_parser.add_argument('-P', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb in input_dir')
 arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_mcsm_snps.csv exists')
 
 # FIXME: Doesn't work with 2 chains yet!
@@ -55,18 +55,19 @@ args = arg_parser.parse_args()
 #gene_match = gene + '_p.'
 #%%=====================================================================
 # Command line options
-drug         = args.drug
-gene         = args.gene
+drug          = args.drug
+gene          = args.gene
 
-datadir      = args.datadir
-indir        = args.input_dir
-outdir       = args.output_dir
-process_dir  = args.process_dir
+datadir       = args.datadir
+indir         = args.input_dir
+outdir        = args.output_dir
+process_dir   = args.process_dir
+
+mut_filename  = args.mutation_file
+chainA        = args.chain1
+chainB        = args.chain2
+pdb_filename  = args.pdb_file
 
-mut_filename = args.mutation_file
-chainA       = args.chain1
-chainB       = args.chain2
-pdb_filename = args.pdb_file
 
 # os.path.splitext will fail interestingly with file.pdb.txt.zip
 #pdb_name = os.path.splitext(pdb_file)[0]