tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

fixed white space prob with mcsm input with merge

Browse source
This commit is contained in:
Tanushree Tunstall 2020-07-14 14:07:23 +01:00
parent 46b1505fdf
commit 7d36e0e36b
6 changed files with 108 additions and 98 deletions
Download patch file Download diff file Expand all files Collapse all files

57
mcsm/run_mcsm.py
View file

@ -18,29 +18,39 @@ arg_parser.add_argument('-c', '--chain', help='Chain ID as per PDB, Case sensi
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('--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('--debug', action='store_true', help = 'Debug Mode')
args = arg_parser.parse_args()
gene = args.gene
drug = args.drug
stage = args.stage
chain = args.chain
ligand = args.ligand
affinity = args.affinity
pdb_filename = args.pdb_file
data_dir = args.data_dir
DEBUG = args.debug
# Actual Globals :-)
host = args.host
prediction_url = args.url
#=======================================================================
#%% variables
#host = "http://biosig.unimelb.edu.au"
#prediction_url = f"{host}/mcsm_lig/prediction"
#drug = 'isoniazid'
#gene = 'KatG'
#%%=====================================================================
# Command line options
gene = args.gene
drug = args.drug
stage = args.stage
chain = args.chain
ligand = args.ligand
affinity = args.affinity
pdb_filename = args.pdb_file
datadir = args.datadir
indir = args.input_dir
outdir = args.output_dir
DEBUG = args.debug
# Actual Globals :-)
host = args.host
prediction_url = args.url
# submit_mcsm globals
homedir = os.path.expanduser('~')
@ -51,13 +61,14 @@ gene_match = gene + '_p.'
#============
# directories
#============
if data_dir:
datadir = data_dir
else:
datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/' + 'input'
outdir = datadir + '/' + drug + '/' + 'output'
if not datadir:
datadir = homedir + '/' + 'git/Data'
if not indir:
indir = datadir + '/' + drug + '/input'
if not outdir:
outdir = datadir + '/' + drug + '/output'
#=======
# input