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

ran struc param analysis

Browse source
This commit is contained in:
Tanushree Tunstall 2020-06-17 19:36:02 +01:00
parent 96da4d8ed5
commit 2cebd338ba
5 changed files with 373 additions and 382 deletions
Download patch file Download diff file Expand all files Collapse all files

10
scripts/dssp_df.py
View file

@ -30,10 +30,8 @@ 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 = 'TESTDRUG')
arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = 'testGene') # 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) # case sensitive
args = arg_parser.parse_args()
#=======================================================================
#%% variable assignment: input and output
@ -49,6 +47,8 @@ args = arg_parser.parse_args()
drug = args.drug
gene = args.gene
gene_match = gene + '_p.'
#==========
# data dir
#==========
@ -147,7 +147,7 @@ def extract_chain_dssp(inputpdbfile):
return pdbchainlist
#=======================================================================
#%% write csv of processed dssp output
def dssp_to_csv(inputdsspfile, outfile, pdbchainlist):
def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']):
"""
Create a df from a dssp file containing ASA, RSA, SS for all chains