tanu/LSHTM_analysis
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Merge branch 'embb_dev'

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Tanushree Tunstall 2021-11-12 14:37:10 +00:00
commit c32de1bf0f
7 changed files with 238 additions and 116 deletions
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61
dynamut/run_format_results_dynamut.py
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@ -17,61 +17,52 @@ os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
from format_results_dynamut import *
from format_results_dynamut2 import *
########################################################################
# variables
# TODO: add cmd line args
#gene =
#drug =
#%% command line args
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('-d', '--drug', help='drug name (case sensitive)', default = None)
arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
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('-d', '--drug' , help = 'drug name (case sensitive)', default = None)
arg_parser.add_argument('-g', '--gene' , help = 'gene name (case sensitive)', default = None)
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('-m', '--make_dirs', help = 'Make dir for input and output', action='store_true') # should be handled elsewhere!
arg_parser.add_argument('--debug', action ='store_true', help = 'Debug Mode')
#arg_parser.add_argument('--mkdir_name' , help = 'Output dir for processed results. This will be created if it does not exist')
arg_parser.add_argument('-m', '--make_dirs' , help = 'Make dir for input and output', action='store_true')
arg_parser.add_argument('--debug' , action = 'store_true' , help = 'Debug Mode')
args = arg_parser.parse_args()
#=======================================================================
#%% variable assignment: input and output paths & filenames
drug = args.drug
gene = args.gene
datadir = args.datadir
indir = args.input_dir
outdir = args.output_dir
#make_dirs = args.make_dirs
#%%============================================================================
# variable assignment: input and output paths & filenames
drug = args.drug
gene = args.gene
datadir = args.datadir
indir = args.input_dir
outdir = args.output_dir
#outdir_dynamut2 = args.mkdir_name
make_dirs = args.make_dirs
#%% input and output dirs and files
#=======
# dirs
#=======
if not datadir:
datadir = homedir + '/' + 'git/Data'
datadir = homedir + '/git/Data/'
if not indir:
indir = datadir + '/' + drug + '/input'
indir = datadir + drug + '/input/'
if not outdir:
outdir = datadir + '/' + drug + '/output'
#%%=====================================================================
datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input'
outdir = datadir + '/' + drug + '/output'
outdir_dynamut = outdir + '/dynamut_results/'
outdir_dynamut2 = outdir + '/dynamut_results/dynamut2/'
outdir = datadir + drug + '/output/'
#if not mkdir_name:
outdir_dynamut = outdir + 'dynamut_results/'
outdir_dynamut2 = outdir + 'dynamut_results/dynamut2/'
# Input file
#infile_dynamut = outdir_dynamut + gene.lower() + '_dynamut_all_output_clean.csv'
infile_dynamut2 = outdir_dynamut2 + gene.lower() + '_dynamut2_output_combined_clean.csv'
# Formatted output filename
#outfile_dynamut_f = outdir_dynamut2 + gene + '_dynamut_norm.csv'
outfile_dynamut2_f = outdir_dynamut2 + gene.lower() + '_dynamut2_norm.csv'
outfile_dynamut_f = outdir_dynamut2 + gene + '_dynamut_norm.csv'
outfile_dynamut2_f = outdir_dynamut2 + gene + '_dynamut2_norm.csv'
#%%========================================================================
#===============================
# CALL: format_results_dynamut