48 lines
1.4 KiB
Python
48 lines
1.4 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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#%% 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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# variables
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# TODO: add cmd line args
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# Imagine we've done the work
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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_na = outdir + '/mcsm_na_results/'
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# Input file
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infile_mcsm_na = outdir_na + gene + '_output_combined_clean.tsv'
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# Formatted output file
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outfile_mcsm_na_f = outdir_na + gene + '_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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#==========================
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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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