Update code/add_alignment.py

code/add_alignment.py

@@ -46,6 +46,7 @@ def do_alignment(identifier, uniprotSequence, pdbSequence, alignment_path):
     
 
 def mutation_position_on_pdb(alignment_list, pos):
+    st.write('Now I am here in mutation_position_on_pdb')
     which_alignment_to_go = 0
     for alignment in alignment_list:
         which_alignment_to_go += 1
@@ -109,6 +110,11 @@ def mutation_position_on_pdb(alignment_list, pos):
         else:
             pdb_alignStatus = 'not_aligned'
             mutationPositionOnPDB = 'nan'
+    st.write('pdb_alignStatus', pdb_alignStatus)
+    st.write('mutationPositionOnPDB', mutationPositionOnPDB)
+    st.write('startGap', startGap)
+    st.write('alignment_list[which_alignment_to_go - 1]', alignment_list[which_alignment_to_go - 1])
+
     return (pdb_alignStatus, mutationPositionOnPDB, startGap, alignment_list[which_alignment_to_go - 1])
 
 
@@ -321,11 +327,13 @@ def annotation_pos_on_pdb(annot_positions, startGap, alignment_to_use, identifie
 
 
 def final_stage(df, annotation_list, alignment_path):
+    st.write('I am here for the error-giving datapoint.')
     for i in df.index:
         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.iloc[i])
         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: