output from comb script & electrostatic mut changes calculated

meta_data_analysis/data_extraction.py

@@ -9,9 +9,9 @@ Created on Tue Aug  6 12:56:03 2019
 # FIXME: include error checking to enure you only
 # concentrate on positions that have structural info?
 
+# FIXME: import dirs.py to get the basic dir paths available
+
 #%% load libraries
-###################
-# load libraries
 import os, sys
 import pandas as pd
 #import numpy as np
@@ -52,19 +52,19 @@ 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
-#=======
+#==========
 #indir = 'git/Data/pyrazinamide/input/original'
 indir = homedir + '/' + 'git/Data'
-#=========
+
+#===========
 # output dir
-#=========
+#===========
 # several output files
 # output filenames in respective sections at the time of outputting files
 #outdir = 'git/Data/pyrazinamide/output'