updated kd.py to relfect a merging col for combining num params later

meta_data_analysis/data_extraction.py

@@ -10,16 +10,7 @@ Created on Tue Aug  6 12:56:03 2019
 # concentrate on positions that have structural info?
 
 # FIXME: import dirs.py to get the basic dir paths available
-
-#%% load libraries
-import os, sys
-import pandas as pd
-#import numpy as np
-
-#from pandas.api.types import is_string_dtype
-#from pandas.api.types import is_numeric_dtype
-
-#========================================================
+#=======================================================================
 # TASK: extract ALL pncA_p. mutations from GWAS data
 # Input data file has the following format: each row = unique sample id 
 # id,country,lineage,sublineage,drtype,pyrazinamide,dr_mutations_pyrazinamide,other_mutations_pyrazinamide...
@@ -38,46 +29,58 @@ import pandas as pd
 # 3) pnca_metadata.csv
 # 4) pnca_all_muts_msa.csv
 # 5) pnca_mutational_positons.csv
-#========================================================
+#=======================================================================
+#%% load libraries
+import os, sys
+import pandas as pd
+#import numpy as np
+
+#from pandas.api.types import is_string_dtype
+#from pandas.api.types import is_numeric_dtype
+
 #%% specify homedir as python doesn't recognise tilde
 homedir = os.path.expanduser('~') 
 
-# my working dir
+# set working dir
 os.getcwd()
 os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
 os.getcwd()
 
 # import aa dict
 from reference_dict import my_aa_dict #CHECK DIR STRUC THERE!
-#========================================================
-
+#=======================================================================
 #%% variable assignment: input and output paths & filenames
 drug = 'pyrazinamide'
 gene = 'pncA'
 gene_match = gene + '_p.'
 
-#==========
-# input dir
-#==========
+#=======
+# data dir
+#=======
 #indir = 'git/Data/pyrazinamide/input/original'
-indir = homedir + '/' + 'git/Data'
+datadir = homedir + '/' + 'git/Data'
 
-#===========
-# output dir
-#===========
+#=======
+# input
+#=======
+#indir = 'git/Data/pyrazinamide/input/original'
+in_filename  = 'original_tanushree_data_v2.csv'
+infile = datadir + '/' + in_filename
+print('Input filename: ', in_filename
+      , '\nInput path: ', indir)
+
+#=======
+# output
+#=======
 # several output files
 # output filenames in respective sections at the time of outputting files
-#outdir = 'git/Data/pyrazinamide/output'
-outdir = homedir + '/' + 'git/Data' + '/' + drug + '/' + 'output'
+outdir = datadir + '/' + drug + '/' + 'output'
+print('Output filename: in the respective sections'
+      , '\nOutput path: ', outdir)
 
 #%%end of variable assignment for input and output files
-#==============================================================================
-#%% Read files
-
-in_filename  = 'original_tanushree_data_v2.csv'
-infile = indir + '/' + in_filename
-print('Reading input master file:', infile)
-
+#=======================================================================
+#%% Read input file
 master_data  = pd.read_csv(infile, sep = ',')  
 
 # column names