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

test2 bugfixes

Browse source
This commit is contained in:
Tanushree Tunstall 2021-02-08 15:24:22 +00:00
parent 7a9b16255a
commit 1f8cfc2403
13 changed files with 851 additions and 69 deletions
Download patch file Download diff file Expand all files Collapse all files

5
foldx/runFoldx.py
View file

@ -35,11 +35,12 @@ arg_parser.add_argument('-g', '--gene', help = 'gene name (case sensitive)',
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('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + <drug> + processing. Make sure it is somewhere with LOTS of storage as it writes all output!')
arg_parser.add_argument('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + <drug> + processing. Make sure it is somewhere with LOTS of storage as it writes all output!') #FIXME
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>_mcsm_snps.csv exists')
# FIXME: Doesn't work with 2 chains yet!
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
@ -101,7 +102,7 @@ actual_pdb_filename = Path(infile_pdb).name
if mut_filename:
mutation_file = mut_filename
else:
mutation_file = gene.lower() + '_mcsm_snps.csv'
mutation_file = gene.lower() + '_mcsm_formatted_snps.csv'
infile_muts = outdir + '/' + mutation_file