From 7a9b16255a47160168bf7f33e344307236c563d4 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Wed, 2 Dec 2020 11:26:26 +0000
Subject: [PATCH] added user defined option for processing dir to allow me to
 specify external storage device for running it

---
 foldx/runFoldx.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/foldx/runFoldx.py b/foldx/runFoldx.py
index 219f421..1538a6c 100755
--- a/foldx/runFoldx.py
+++ b/foldx/runFoldx.py
@@ -35,9 +35,10 @@ arg_parser.add_argument('-g', '--gene',     help = 'gene name (case sensitive)',
 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('-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!')
 
 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('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_snps.csv exists')
+arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_mcsm_snps.csv exists')
 
 arg_parser.add_argument('-c1', '--chain1',    help = 'Chain1 ID', default = 'A') # case sensitive
 arg_parser.add_argument('-c2', '--chain2',    help = 'Chain2 ID', default = 'B') # case sensitive
@@ -56,6 +57,7 @@ gene         = args.gene
 datadir      = args.datadir
 indir        = args.input_dir
 outdir       = args.output_dir
+process_dir  = args.process_dir
 
 mut_filename = args.mutation_file
 chainA       = args.chain1
@@ -79,10 +81,10 @@ if not indir:
 if not outdir:
     outdir = datadir + '/' + drug + '/output'
 
-# FIXME: this is a temporary directory and should be correctly handled
-process_dir = datadir + '/' + drug +'/' + 'processing'
+#TODO: perhaps better handled by refactoring code to prevent generating lots of output files!
+if not process_dir:
+    process_dir = datadir + '/' + drug +'/' + 'processing'
 
-#os.mkdir(process_dir)
 #=======
 # input
 #=======