tidied and updated kd and dssp scripts & generated their respective outputs

meta_data_analysis/init_data_dirs.py

@@ -5,3 +5,32 @@
 # - Create eg: '~/git/Data/{original,processed}
 # - Create eg: '~/git/Data/processed/' + drug (for each drug)
 # - Create eg: '~/git/Data/output/' + drug + '{plots, structure}'
+
+
+#%% specify homedir as python doesn't recognise tilde
+homedir = os.path.expanduser('~') 
+
+#%% variable assignment: input and output paths & filenames
+drug = 'pyrazinamide'
+gene = 'pncA'
+gene_match = gene + '_p.'
+
+#==========
+# data dir
+#==========
+#indir = 'git/Data/pyrazinamide/input/original'
+datadir = homedir + '/' + 'git/Data'
+
+#==========
+# input dir
+#==========
+indir = datadir + '/' + drug + '/' + 'input'
+
+#============
+# output dir
+#============
+# several output files
+outdir = datadir + '/' + drug + '/' + 'output'
+
+#%%end of variable assignment for input and output files
+#==============================================================================