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added user defined option for processing dir to allow me to specify external storage device for running it

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Tanushree Tunstall 2020-12-02 11:26:26 +00:00
parent 08ad16adbb
commit 7a9b16255a
1 changed files with 6 additions and 4 deletions
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10
foldx/runFoldx.py
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@ -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('--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('-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('-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('-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('-c1', '--chain1', help = 'Chain1 ID', default = 'A') # case sensitive
arg_parser.add_argument('-c2', '--chain2', help = 'Chain2 ID', default = 'B') # 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 datadir = args.datadir
indir = args.input_dir indir = args.input_dir
outdir = args.output_dir outdir = args.output_dir
process_dir = args.process_dir
mut_filename = args.mutation_file mut_filename = args.mutation_file
chainA = args.chain1 chainA = args.chain1
@ -79,10 +81,10 @@ if not indir:
if not outdir: if not outdir:
outdir = datadir + '/' + drug + '/output' outdir = datadir + '/' + drug + '/output'
# FIXME: this is a temporary directory and should be correctly handled #TODO: perhaps better handled by refactoring code to prevent generating lots of output files!
process_dir = datadir + '/' + drug +'/' + 'processing' if not process_dir:
process_dir = datadir + '/' + drug +'/' + 'processing'
#os.mkdir(process_dir)
#======= #=======
# input # input
#======= #=======