added script for formatting mcsm_na results

mcsm_na/run_format_results_mcsm_na.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Feb 12 12:15:26 2021
+
+@author: tanu
+"""
+#%% load packages
+import os
+homedir = os.path.expanduser('~')
+os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
+from format_results_mcsm_na import *
+########################################################################
+# variables
+
+# TODO: add cmd line args
+
+#gene = 'gid'
+drug = 'streptomycin'
+datadir = homedir + '/git/Data'
+indir = datadir + '/' + drug + '/input'
+outdir = datadir + '/' + drug + '/output'
+outdir_na = outdir + '/mcsm_na_results/'
+
+# Input file
+infile_mcsm_na =  outdir_na + 'gid_output_combined_clean.tsv'
+
+# Formatted output file
+outfile_mcsm_na_f = outdir_na + 'gid_complex_mcsm_na_norm.csv'
+
+#==========================
+# CALL: format_results_mcsm_na() 
+# Data: gid+streptomycin
+#==========================
+print('Formatting results for:', infile_mcsm_na)
+mcsm_na_df_f = format_mcsm_na_output(mcsm_na_output_tsv = infile_mcsm_na)
+
+# writing file
+print('Writing formatted df to csv')
+mcsm_na_df_f.to_csv(outfile_mcsm_na_f, index = False)
+
+print('Finished writing file:'
+       , '\nFile:', outfile_mcsm_na_f
+       , '\nExpected no. of rows:', len(mcsm_na_df_f)
+       , '\nExpected no. of cols:', len(mcsm_na_df_f.columns)
+       , '\n=============================================================')
+
+#%%#####################################################################