added dynamut results formatting scripts, althouh needs to be rerun once b7 completes

dynamut/run_format_results_dynamut.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Feb 12 12:15:26 2021
+
+@author: tanu
+"""
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+# FIXME 
+# RE RUN when B07 completes!!!! as norm gets affected!
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+#%% load packages
+import os
+homedir = os.path.expanduser('~')
+os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
+from format_results_dynamut import *
+########################################################################
+# variables
+
+# TODO: add cmd line args
+
+gene = 'gid'
+drug = 'streptomycin'
+datadir = homedir + '/git/Data'
+indir = datadir + '/' + drug + '/input'
+outdir = datadir + '/' + drug + '/output'
+outdir_dynamut = outdir + '/dynamut_results/'
+
+# Input file
+infile_dynamut =  outdir_dynamut + gene + '_dynamut_all_output_clean.csv'
+
+# Formatted output filename
+outfile_dynamut_f = outdir_dynamut + gene + '_complex_dynamut_norm.csv'
+
+#==========================
+# CALL: format_results_mcsm_na() 
+# Data: gid+streptomycin
+#==========================
+print('Formatting results for:', infile_dynamut)
+dynamut_df_f = format_dynamut_output(dynamut_output_csv = infile_dynamut)
+
+# writing file
+print('Writing formatted dynamut df to csv')
+dynamut_df_f.to_csv(outfile_dynamut_f, index = False)
+
+print('Finished writing file:'
+       , '\nFile:', outfile_dynamut_f
+       , '\nExpected no. of rows:', len(dynamut_df_f)
+       , '\nExpected no. of cols:', len(dynamut_df_f.columns)
+       , '\n=============================================================')
+
+#%%#####################################################################