72 lines
No EOL
2.4 KiB
Python
72 lines
No EOL
2.4 KiB
Python
#!/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 = 'gid'
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drug = 'streptomycin'
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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 + '_complex_dynamut_norm.csv'
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outfile_dynamut2_f = outdir_dynamut2 + gene + '_complex_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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#%%##################################################################### |