#!/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=============================================================')

#%%#####################################################################