78 lines
2.9 KiB
Python
Executable file
78 lines
2.9 KiB
Python
Executable file
#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Feb 12 12:15:26 2021
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@author: tanu
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"""
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#%% load packages
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import os
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homedir = os.path.expanduser('~')
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os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
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from format_results_mcsm_na import *
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########################################################################
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#%% command line args
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arg_parser = argparse.ArgumentParser()
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arg_parser.add_argument('-d', '--drug' , help = 'drug name (case sensitive)', default = None)
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arg_parser.add_argument('-g', '--gene' , help = 'gene name (case sensitive)', default = None)
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arg_parser.add_argument('--datadir' , help = 'Data Directory. By default, it assmumes homedir + git/Data')
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arg_parser.add_argument('-i', '--input_dir' , help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
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arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
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#arg_parser.add_argument('--mkdir_name' , help = 'Output dir for processed results. This will be created if it does not exist')
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arg_parser.add_argument('-m', '--make_dirs' , help = 'Make dir for input and output', action='store_true')
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arg_parser.add_argument('--debug' , action = 'store_true' , help = 'Debug Mode')
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args = arg_parser.parse_args()
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#%%============================================================================
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# variable assignment: input and output paths & filenames
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drug = args.drug
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gene = args.gene
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datadir = args.datadir
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indir = args.input_dir
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outdir = args.output_dir
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#outdir_ppi2 = args.mkdir_name
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make_dirs = args.make_dirs
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#=======
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# dirs
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#=======
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if not datadir:
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datadir = homedir + '/git/Data/'
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if not indir:
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indir = datadir + drug + '/input/'
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if not outdir:
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outdir = datadir + drug + '/output/'
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#if not mkdir_name:
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# outdir_na = outdir + 'mcsm_na_results/'
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outdir_na = outdir + 'mcsm_na_results/'
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# Input file
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infile_mcsm_na = outdir_na + gene.lower() + '_output_combined_clean.tsv'
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# Formatted output file
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outfile_mcsm_na_f = outdir_na + gene.lower() + '_complex_mcsm_na_norm.csv'
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#===========================================
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# CALL: format_results_mcsm_na()
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# Data: gid+streptomycin
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# Data: rpob+rifampicin, date: 18/11/2021
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#===========================================
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print('Formatting results for:', infile_mcsm_na)
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mcsm_na_df_f = format_mcsm_na_output(mcsm_na_output_tsv = infile_mcsm_na)
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# writing file
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print('Writing formatted df to csv')
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mcsm_na_df_f.to_csv(outfile_mcsm_na_f, index = False)
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print('Finished writing file:'
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, '\nFile:', outfile_mcsm_na_f
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, '\nExpected no. of rows:', len(mcsm_na_df_f)
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, '\nExpected no. of cols:', len(mcsm_na_df_f.columns)
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, '\n=============================================================')
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#%%#####################################################################
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