Update code/add_alignment.py

code/add_alignment.py

@@ -341,10 +341,7 @@ def final_stage(df, annotation_list, alignment_path):
         print('i',identifier)
         alignment_list = do_alignment(identifier, df.at[i, 'uniprotSequence'], df.at[i, 'pdbSequence'], alignment_path)
         df.at[i, 'pdb_alignStatus'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[0]
-        
-        print('df',df)        
-        df.at[i, 'mutationPositionOnPDB'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[1]
-        print('df',df)
+                df.at[i, 'mutationPositionOnPDB'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[1]
         startGap = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[2]
         alignment_to_use = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[3]
         for annot in annotation_list:
@@ -360,7 +357,8 @@ def final_stage(df, annotation_list, alignment_path):
                 str(df.at[i, 'domStart']) != '-1.0' or str(df.at[i, 'domEnd']) != '-1.0':
             df.at[i, 'domainStartonPDB'] = 'nan'
             df.at[i, 'domainEndonPDB'] = 'nan'
-    print('df_fin',df)
+    print('Final Stage')
+    print(df)
     return df
 
 def alignment(dataframe_to_align, annotation_list, alignment_path):