Update code/alphafold_featureVector.py

code/alphafold_featureVector.py

@@ -259,7 +259,6 @@ def alphafold(input_set, mode, impute):
             wt = uniprot_matched.at[i, 'wt']
             can = str(uniprot_matched.at[i, 'uniprotSequence'])[int(uniprot_matched.at[i, 'pos']) - 1]
             ## Information about whether the mutation is found on the canonical or isoform sequence.
-
             if wt == can:
                 uniprot_matched.at[i, 'wt_sequence_match'] = 'm'
             elif wt != can:
@@ -343,11 +342,15 @@ def alphafold(input_set, mode, impute):
             except:
                 ValueError
                 pdbSequence = 'nan'
+            st.write('SENTIMENTAL')
             if pdbSequence != 'nan':  # The number in models we need might not be present for that protein. Preventng error.
                 pdbSequence = pdb_info.loc[(pdb_info.uniprotID == uniprotID) & (pdb_info.model_num == mod)].sequence.item()
                 alignment_list = do_alignment(uniprot_matched.at[i, 'datapoint'], uniprot_matched.at[i, 'uniprotSequence'],
                                               pdbSequence, Path(path_to_output_files / 'alignment_files'))
+                st.write('alignment_list')
+                st.write(alignment_list)
                 pdb_alignStatus = mutation_position_on_pdb(alignment_list, uniprot_matched.at[i, 'pos'])[0]
+                st.write('alignment_list---')
                 info_per_model[mod]['pdb_alignStatus'] = pdb_alignStatus
                 mutationPositionOnPDB = mutation_position_on_pdb(alignment_list, uniprot_matched.at[i, 'pos'])[1]
                 info_per_model[mod]['mutationPositionOnPDB'] = mutationPositionOnPDB