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adding default dirs and filenames to argparse in foldx and mcsm

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Tanushree Tunstall 2020-07-09 12:57:08 +01:00
parent 6402990154
commit f8e345f5bc
3 changed files with 35 additions and 28 deletions
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28
foldx/runFoldx.py
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@ -29,16 +29,16 @@ os.getcwd()
#%% command line args
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('-d', '--drug', help = 'drug name', default = 'pyrazinamide')
arg_parser.add_argument('-g', '--gene', help = 'gene name', default = 'pncA') # case sensitive
arg_parser.add_argument('-d', '--drug', help = 'drug name', default = None)
arg_parser.add_argument('-g', '--gene', help = 'gene name (case sensitive)', default = None)
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('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + drug + input', default = None)
arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + drug + output', default = None)
arg_parser.add_argument('-f', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb', default = None)
arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_snps.csv exists', default = None)
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('-c1', '--chain1', help = 'Chain1 ID', default = 'A') # case sensitive
arg_parser.add_argument('-c2', '--chain2', help = 'Chain2 ID', default = 'B') # case sensitive
@ -53,8 +53,11 @@ args = arg_parser.parse_args()
# Command Line Options
drug = args.drug
gene = args.gene
data_dir = args.data_dir
indir = args.input_dir
outdir = args.output_dir
mut_filename = args.mutation_file
chainA = args.chain1
chainB = args.chain2
@ -68,13 +71,17 @@ pdb_filename = args.pdb_file
#==========
# dir
#==========
datadir = homedir + '/' + 'git/Data'
if data_dir:
datadir = data_dir
else:
datadir = homedir + '/' + 'git/Data'
if not indir:
indir = datadir + '/' + drug + '/' + 'input'
if not outdir:
outdir = datadir + '/' + drug + '/' + 'output'
# FIXME: this is a temporary directory and should be correctly handled
process_dir = datadir + '/' + drug +'/' + 'processing'
@ -96,8 +103,7 @@ actual_pdb_filename = Path(infile_pdb).name
if mut_filename:
mutation_file = mut_filename
else:
mutation_file = gene.lower() + '_mcsm_snps.csv' #real
#mutation_file = gene.lower() + '_test_snps.csv' #test
mutation_file = gene.lower() + '_mcsm_snps.csv'
infile_muts = outdir + '/' + mutation_file