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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 44597ec563
commit 08379c0def
3 changed files with 19 additions and 10 deletions
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6
foldx/runFoldx.py
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@ -68,9 +68,9 @@ pdb_filename = args.pdb_file
# Just the filename, thanks # Just the filename, thanks
#pdb_name = Path(in_filename_pdb).stem #pdb_name = Path(in_filename_pdb).stem
#========== #============
# dir # directories
#========== #============
if data_dir: if data_dir:
datadir = data_dir datadir = data_dir
else: else:

13
mcsm/run_mcsm.py
View file

@ -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('-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('-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('-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('-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', default = 0.99) 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('-pdb','--pdb_file', help = 'PDB File')
arg_parser.add_argument('--datadir', help = 'Data Directory') arg_parser.add_argument('--datadir', help = 'Data Directory')
arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode') 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') #os.chdir(homedir + '/git/LSHTM_analysis/mcsm')
gene_match = gene + '_p.' gene_match = gene + '_p.'
#============
# directories
#============
if data_dir: if data_dir:
datadir = data_dir datadir = data_dir
else: else:
@ -56,6 +59,9 @@ else:
indir = datadir + '/' + drug + '/' + 'input' indir = datadir + '/' + drug + '/' + 'input'
outdir = datadir + '/' + drug + '/' + 'output' outdir = datadir + '/' + drug + '/' + 'output'
#=======
# input
#=======
if pdb_filename: if pdb_filename:
in_filename_pdb = pdb_filename in_filename_pdb = pdb_filename
else: 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) in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile_mcsm_snps, from data_extraction.py)
infile_snps = outdir + '/' + in_filename_snps infile_snps = outdir + '/' + in_filename_snps
#=======
# output
#=======
# mcsm_results globals # mcsm_results globals
result_urls_filename = gene.lower() + '_result_urls.txt' result_urls_filename = gene.lower() + '_result_urls.txt'
result_urls = outdir + '/' + result_urls_filename result_urls = outdir + '/' + result_urls_filename

10
scripts/dssp_df.py
View file

@ -60,9 +60,9 @@ pdb_filename = args.pdb_file
DEBUG = args.debug DEBUG = args.debug
#========== #=============
# dirs # directories
#========== #=============
if data_dir: if data_dir:
datadir = data_dir datadir = data_dir
else: else:
@ -204,8 +204,8 @@ def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']):
#======================================================================= #=======================================================================
def main(): def main():
print('Running dssp with the following params:\n' print('Running dssp with the following params:\n'
, '\ninput pdb:', in_filename_pdb , '\nInput pdb file:', in_filename_pdb
, '\noutfile:', out_filename_dssp_csv) , '\nOutput:', out_filename_dssp_csv)
dssp_file_from_pdb(infile_pdb, dssp_file, DSSP = "dssp") dssp_file_from_pdb(infile_pdb, dssp_file, DSSP = "dssp")
my_chains = extract_chain_dssp(infile_pdb) my_chains = extract_chain_dssp(infile_pdb)
dssp_to_csv(dssp_file, outfile_dssp_csv, my_chains) dssp_to_csv(dssp_file, outfile_dssp_csv, my_chains)