109 lines
3.8 KiB
Python
Executable file
109 lines
3.8 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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#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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# FIXME
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# RE RUN when B07 completes!!!! as norm gets affected!
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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/dynamut')
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from format_results_dynamut import *
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from format_results_dynamut2 import *
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########################################################################
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# variables
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# TODO: add cmd line args
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#gene =
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#drug =
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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('-m', '--make_dirs', help = 'Make dir for input and output', action='store_true') # should be handled elsewhere!
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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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#make_dirs = args.make_dirs
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#%% input and output dirs and files
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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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#%%=====================================================================
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datadir = homedir + '/git/Data'
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indir = datadir + '/' + drug + '/input'
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outdir = datadir + '/' + drug + '/output'
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outdir_dynamut = outdir + '/dynamut_results/'
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outdir_dynamut2 = outdir + '/dynamut_results/dynamut2/'
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# Input file
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#infile_dynamut = outdir_dynamut + gene + '_dynamut_all_output_clean.csv'
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infile_dynamut2 = outdir_dynamut2 + gene + '_dynamut2_output_combined_clean.csv'
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# Formatted output filename
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#outfile_dynamut_f = outdir_dynamut2 + gene + '_dynamut_norm.csv'
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outfile_dynamut2_f = outdir_dynamut2 + gene + '_dynamut2_norm.csv'
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#===============================
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# CALL: format_results_dynamut
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# DYNAMUT results
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# #===============================
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# print('Formatting results for:', infile_dynamut)
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# dynamut_df_f = format_dynamut_output(infile_dynamut)
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# # writing file
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# print('Writing formatted dynamut df to csv')
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# dynamut_df_f.to_csv(outfile_dynamut_f, index = False)
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# print('Finished writing file:'
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# , '\nFile:', outfile_dynamut_f
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# , '\nExpected no. of rows:', len(dynamut_df_f)
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# , '\nExpected no. of cols:', len(dynamut_df_f.columns)
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# , '\n=============================================================')
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#===============================
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# CALL: format_results_dynamut2
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# DYNAMUT2 results
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#===============================
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print('Formatting results for:', infile_dynamut2)
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dynamut2_df_f = format_dynamut2_output(infile_dynamut2) # dynamut2
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# writing file
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print('Writing formatted dynamut2 df to csv')
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dynamut2_df_f.to_csv(outfile_dynamut2_f, index = False)
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print('Finished writing file:'
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, '\nFile:', outfile_dynamut2_f
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, '\nExpected no. of rows:', len(dynamut2_df_f)
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, '\nExpected no. of cols:', len(dynamut2_df_f.columns)
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, '\n=============================================================')
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#%%#####################################################################
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