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minor tidy up in foldx, mcsm and dssp scripts

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This commit is contained in:
Tanushree Tunstall 2020-07-09 14:04:16 +01:00
parent 0379d3e241
commit e4a7deae7b
3 changed files with 19 additions and 10 deletions
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13
mcsm/run_mcsm.py
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@ -15,8 +15,8 @@ arg_parser.add_argument('-s', '--stage', help='mCSM Pipeline Stage', default =
arg_parser.add_argument('-H', '--host', help='mCSM Server', default = 'http://biosig.unimelb.edu.au')
arg_parser.add_argument('-U', '--url', help='mCSM Server URL', default = 'http://biosig.unimelb.edu.au/mcsm_lig/prediction')
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('-l','--ligand', help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage', default = None)
arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 0.99)
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')
@ -48,6 +48,9 @@ homedir = os.path.expanduser('~')
#os.chdir(homedir + '/git/LSHTM_analysis/mcsm')
gene_match = gene + '_p.'
#============
# directories
#============
if data_dir:
datadir = data_dir
else:
@ -56,6 +59,9 @@ else:
indir = datadir + '/' + drug + '/' + 'input'
outdir = datadir + '/' + drug + '/' + 'output'
#=======
# input
#=======
if pdb_filename:
in_filename_pdb = pdb_filename
else:
@ -66,6 +72,9 @@ infile_pdb = indir + '/' + in_filename_pdb
in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile_mcsm_snps, from data_extraction.py)
infile_snps = outdir + '/' + in_filename_snps
#=======
# output
#=======
# mcsm_results globals
result_urls_filename = gene.lower() + '_result_urls.txt'
result_urls = outdir + '/' + result_urls_filename