Update code/add_alignment.py

code/add_alignment.py

@@ -306,10 +306,12 @@ def annotation_pos_on_pdb(annot_positions, startGap, alignment_to_use, identifie
 
 def final_stage(df, annotation_list, alignment_path):
     for i in df.index:
+        st.write('i',i)
         identifier = df.at[i, 'uniprotID'] + '_' + df.at[i, 'pdbID'] + '_' + df.at[i, 'chain'] + '_'
         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]
         df.at[i, 'mutationPositionOnPDB'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[1]
+        st.write('df',df)
         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:
@@ -325,6 +327,7 @@ 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'
+    st.write('df_fin',df)
     return df
 
 def alignment(dataframe_to_align, annotation_list, alignment_path):