diff --git a/scripts/combine_dfs.py b/scripts/combine_dfs.py
new file mode 100755
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+++ b/scripts/combine_dfs.py
@@ -0,0 +1,301 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+'''
+Created on Tue Aug  6 12:56:03 2019
+
+@author: tanu
+'''
+# FIXME: change filename 4 (mcsm normalised data)
+# to be consistent like (pnca_complex_mcsm_norm.csv) : changed manually, but ensure this is done in the mcsm pipeline
+#=============================================================================
+# Task: combine 4 dfs with aa position as linking column
+# This is done in 2 steps:
+# merge 1: of 3 dfs (filenames in lowercase)
+#   <gene.lower()>_dssp.csv
+#   <gene.lower()>_kd.csv
+#   <gene.lower()>_pnca_rd.csv
+
+# merge 2: of 2 dfs
+#    pnca_complex_mcsm_norm.csv (!fix name)
+#    output df from merge1
+
+# Input: 3 dfs
+#   <gene.lower()>_dssp.csv
+#   <gene.lower()>_kd.csv
+#   <gene.lower()>_pnca_rd.csv
+# pnca_complex_mcsm_norm.csv (!fix name)
+
+# Output: .csv of all 4 dfs combined
+
+# useful link
+# https://stackoverflow.com/questions/23668427/pandas-three-way-joining-multiple-dataframes-on-columns
+#=============================================================================
+#%% load packages
+import sys, os
+import pandas as pd
+#import numpy as np
+import argparse
+#=======================================================================
+#%% specify input and curr dir
+homedir = os.path.expanduser('~')
+
+# set working dir
+os.getcwd()
+os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
+os.getcwd()
+#=======================================================================
+#%% command line args
+arg_parser = argparse.ArgumentParser()
+#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazin')
+arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pn') # case sensitive
+args = arg_parser.parse_args()
+#=======================================================================
+#%% variable assignment: input and output 
+#drug = 'pyrazinamide'
+#gene = 'pncA'
+#gene_match = gene + '_p.'
+
+drug = args.drug
+gene = args.gene
+#==========
+# data dir
+#==========
+datadir = homedir + '/' + 'git/Data'
+
+#=======
+# input
+#=======
+indir = datadir + '/' + drug + '/' + 'output'
+in_filename1 = 'pnca_dssp.csv'
+in_filename2 = 'pnca_kd.csv'
+in_filename3 = 'pnca_rd.csv'
+#in_filename4 = 'mcsm_complex1_normalised.csv' # FIXNAME
+in_filename4 = 'pnca_complex_mcsm_norm.csv' 
+
+infile1 = indir + '/' + in_filename1
+infile2 = indir + '/' + in_filename2
+infile3 = indir + '/' + in_filename3
+infile4 = indir + '/' + in_filename4
+
+print('\nInput path:', indir
+      , '\nInput filename1:', in_filename1
+      , '\nInput filename2:', in_filename2
+      , '\nInput filename3:', in_filename3
+      , '\nInput filename4:', in_filename4
+      , '\n===================================================================')
+
+#=======
+# output 
+#=======
+outdir =   datadir + '/' + drug + '/' + 'output'
+out_filename = gene.lower() + '_mcsm_struct_params.csv'
+outfile =  outdir + '/' + out_filename
+print('Output filename:', out_filename
+      , '\nOutput path:', outdir
+      , '\n===================================================================')
+
+#%% end of variable assignment for input and output files
+#=======================================================================
+#%% function/methd to combine 4 dfs
+
+def combine_dfs(dssp_csv, kd_csv, rd_csv, mcsm_csv, out_combined_csv):
+	"""
+	Combine 4 dfs
+
+	@param dssp_df: csv file (output from dssp_df.py)
+	@type dssp_df: string
+
+	@param kd_df: csv file (output from kd_df.py)
+	@type ks_df: string
+		
+	@param rd_df: csv file (output from rd_df.py)
+	@type rd_df: string
+
+	# FIXME
+	@param mcsm_df: csv file (output of mcsm pipeline)CHECK}
+	@type mcsm_df: string
+
+	@param out_combined_csv: csv file output
+	@type out_combined_csv: string
+		
+	@return:  none, writes combined df as csv
+	"""
+	#========================
+	# read input csv files to combine
+	#========================
+	dssp_df = pd.read_csv(dssp_csv, sep = ',')
+	kd_df = pd.read_csv(kd_csv, sep = ',')
+	rd_df = pd.read_csv(rd_csv, sep = ',')
+	mcsm_df = pd.read_csv(mcsm_csv, sep = ',')
+
+	print('Reading input files:'
+		  , '\ndssp file:', dssp_csv
+		  , '\nNo. of rows:', len(dssp_df)
+		  , '\nNo. of cols:', len(dssp_df.columns)
+		  , '\nColumn names:', dssp_df.columns
+		  , '\n==================================================================='
+		  , '\nkd file:', kd_csv
+		  , '\nNo. of rows:', len(kd_df)
+		  , '\nNo. of cols:', len(kd_df.columns)
+		  , '\nColumn names:', kd_df.columns
+		  , '\n==================================================================='
+		  , '\nrd file:', rd_csv
+		  , '\nNo. of rows:', len(rd_df)
+		  , '\nNo. of cols:', len(rd_df.columns)
+		  , '\nColumn names:', rd_df.columns
+		  , '\n==================================================================='
+		  , '\nrd file:', mcsm_csv
+		  , '\nNo. of rows:', len(mcsm_df)
+		  , '\nNo. of cols:', len(mcsm_df.columns)
+		  , '\nColumn names:', mcsm_df.columns
+		  , '\n===================================================================')
+	
+	#========================
+	# merge 1 (combined_df1)
+	# concatenating 3dfs:
+	# dssp_df, kd_df, rd_df
+	#========================
+	print('starting first merge...\n')
+
+	# checking no. of rows
+	print('Checking if no. of rows of the 3 dfs are equal:\n'
+		  , len(dssp_df) == len(kd_df) == len(rd_df)
+		  , '\nReason: fasta files and pdb files vary since not all pos are part of the structure'
+		  , '\n===================================================================')
+
+	# variables for sanity checks
+	expected_rows_df1 = max(len(dssp_df), len(kd_df), len(rd_df))
+	# beware of harcoding! used for sanity check
+	ndfs = 3
+	ncol_merge = 1
+	offset = ndfs- ncol_merge
+	expected_cols_df1 = len(dssp_df.columns) + len(kd_df.columns) + len(rd_df.columns) - offset
+
+	print('Merge 1:'
+		  , '\ncombining 3dfs by commom col: position'
+		  , '\nExpected nrows in combined_df:', expected_rows_df1
+		  , '\nExpected ncols in combined_df:', expected_cols_df1
+		  , '\nResetting the common col as the index'
+		  , '\n===================================================================')
+
+	#dssp_df.set_index('position', inplace = True)
+	#kd_df.set_index('position', inplace = True)
+	#rd_df.set_index('position', inplace =True)
+
+	#combined_df = pd.concat([dssp_df, kd_df, rd_df], axis = 1, sort = False).reset_index()
+	#combined_df.rename(columns = {'index':'position'})
+
+	combined_df1  = pd.concat(
+		(my_index.set_index('position') for my_index in [dssp_df, kd_df, rd_df])
+		, axis = 1, join = 'outer').reset_index()
+
+	# sanity check
+	print('Checking dimensions of concatenated df1...')
+	if len(combined_df1) == expected_rows_df1 and len(combined_df1.columns) == expected_cols_df1:
+		print('PASS: combined df has expected dimensions'
+		      , '\nNo. of rows in combined df:', len(combined_df1)
+		      , '\nNo. of cols in combined df:', len(combined_df1.columns)
+		      , '\n===============================================================')
+	else:
+		print('FAIL: combined df does not have expected dimensions'
+		      , '\nNo. of rows in combined df:', len(combined_df1)
+		      , '\nNo. of cols in combined df:', len(combined_df1.columns)
+		      , '\n===============================================================')
+
+	#========================
+	# merge 2 (combined_df2)
+	# concatenating 2dfs: 
+	# mcsm_df, combined_df1 (result of merge1)
+	# sort the cols
+	#========================
+	print('starting second merge...\n')
+	
+	# rename col 'Position' in mcsm_df to lowercase 'position'
+	# as it matches the combined_df1 colname to perfom merge
+	
+	#mcsm_df.columns
+	#mcsm_df.rename(columns = {'Position':'position'}) # not working!
+	# copy 'Position' column with the correct colname 
+	print('Firstly, copying \'Position\' col and renaming \'position\' to allow merging'
+		  , '\nNo. of cols before copying: ', len(mcsm_df.columns))
+
+	mcsm_df['position'] = mcsm_df['Position']
+	print('No. of cols after copying: ', len(mcsm_df.columns))
+
+	# sanity check
+	if mcsm_df['position'].equals(mcsm_df['Position']):
+		print('PASS: Copying worked correctly'
+		      , '\ncopied col matches original column'
+		      , '\n===============================================================')
+	else:
+		print('FAIL: copied col does not match original column'
+		     , '\n================================================================')
+
+	# variables for sanity checks
+	expected_rows_df2 = len(mcsm_df)
+	# beware of harcoding! used for sanity check
+	ndfs = 2
+	ncol_merge = 1
+	offset = ndfs - ncol_merge
+	expected_cols_df2 = len(mcsm_df.columns) + len(combined_df1.columns) - offset
+
+	print('Merge 2:'
+		  , '\ncombining 2dfs by commom col: position'
+		  , '\nExpected nrows in combined_df:', expected_rows_df2
+		  , '\nExpected ncols in combined_df:', expected_cols_df2
+		  , '\n===================================================================')
+
+	combined_df2 = mcsm_df.merge(combined_df1, on = 'position')
+
+	# sanity check
+	print('Checking dimensions of concatenated df2...')
+	if len(combined_df2) == expected_rows_df2 and len(combined_df2.columns) == expected_cols_df2:
+		print('PASS: combined df2 has expected dimensions'
+		      , '\nNo. of rows in combined df:', len(combined_df2)
+		      , '\nNo. of cols in combined df:', len(combined_df2.columns)
+		      , '\n===============================================================')
+	else:
+		print('FAIL: combined df2 does not have expected dimensions'
+		      , '\nNo. of rows in combined df:', len(combined_df2)
+		      , '\nNo. of cols in combined df:', len(combined_df2.columns)
+		      , '\n===============================================================')
+		
+	#===============
+	# writing file
+	#===============
+	print('Writing file:'
+		  , '\nFilename:', out_combined_csv
+#		  , '\nPath:',  outdir
+		  , '\nExpected no. of rows:', len(combined_df2)
+		  , '\nExpected no. of cols:', len(combined_df2.columns)
+		  , '\n=========================================================')
+
+	combined_df2.to_csv(out_combined_csv, header = True, index = False)
+
+#%% end of function
+#=======================================================================
+#%% call function
+#combine_dfs(infile1, infile2, infile3, infile4, outfile)
+#=======================================================================
+def main():
+	print('Combining 4 dfs:\n'
+		, in_filename1, '\n'
+		, in_filename2, '\n'
+		, in_filename3, '\n'
+		, in_filename4, '\n'
+		, 'output csv:', out_filename)
+	combine_dfs(infile1, infile2, infile3, infile4, outfile)
+	print('Finished Writing file:'
+		, '\nFilename:', out_filename
+		, '\nPath:',  outdir
+##		, '\nNo. of rows:', ''
+##		, '\nNo. of cols:', ''
+		, '\n===========================================================')
+
+if __name__ == '__main__':
+    main()
+#%% end of script
+#=======================================================================
+