Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -248,10 +248,11 @@ def pdb(input_set, mode, impute):
                     seqs[i[2]] += i[4:]
                 else:
                     seqs[i[2]]  = i[4:]
-            st.write('SEQUENCE PDB')
-            st.write(seqs)
+
             for key, val in seqs.items():
                 seqs[key] = ''.join([threeToOne(i) for i in val])
+            st.write('SEQUENCE PDB')
+            st.write(seqs)
             pdb_data_list = [i for i in pdb_data_list if i.startswith('DBREF')]
             pdb_data_list = [[list(filter(None,i.split(' '))) for j in i.split(' ') if j == 'UNP'] for i in pdb_data_list]
             pdb_data_list = [i for i in pdb_data_list if i != []]
@@ -442,11 +443,7 @@ def pdb(input_set, mode, impute):
         aligned_m = final_stage(dfM, annotation_list, Path(path_to_output_files / 'alignment_files'))
         aligned_nm = final_stage(dfNM, annotation_list, Path(path_to_output_files / 'alignment_files'))
         
-        st.write('aligned_m')
-        st.write(aligned_m)
-        
-        st.write('aligned_nm')
-        st.write(aligned_nm)
+
         
         # When PDB sequence is nan, it is wrongly aligned to the UniProt sequence. Fix them.
         for i in aligned_m.index: