Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -163,7 +163,8 @@ def pdb(input_set, mode, impute):
                             data.at[i, 'wt_sequence_match'] = 'i'
                             data.at[i, 'whichIsoform'] = whichIsoform
                             break
-    
+        print('MATCHING UNIPTOR')
+        print(data.to_string())
         data.wt_sequence_match = data.wt_sequence_match.astype('str')
         data.replace({'': 'nan'}, inplace=True)
         data_size = len(data.drop_duplicates(['datapoint']))
@@ -287,6 +288,11 @@ def pdb(input_set, mode, impute):
                         pdb_info.at[index, 'chain'] = chain_id
                         pdb_info.at[index, 'resolution'] = resolution
                         index += 1
+
+        print('PDB INFO')
+        print(pdb_info.to_string())
+        print('PDB FASTA')
+        print(pdb_fasta.to_string())
         print('PDB file processing finished..')
         for filename in list(Path(path_to_output_files / 'pdb_structures').glob("*")):
             try:
@@ -426,12 +432,18 @@ def pdb(input_set, mode, impute):
         with_pdb_size = len(with_pdb.drop_duplicates(['datapoint']))
         with_pdb = None
 
-        
+        print('dfM')
+        print(dfM.to_string())
+        print('dfNM')
+        print(dfNM)
         print('Aligning sequences...\n')
         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'))
 
-
+        print('aligned_m')
+        print(aligned_m.to_string())
+        print('aligned_nm')
+        print(aligned_nm.to_string())
         
         
         # When PDB sequence is nan, it is wrongly aligned to the UniProt sequence. Fix them.
@@ -474,7 +486,10 @@ def pdb(input_set, mode, impute):
         yes_pdb_no_match = after_up_pdb_alignment[
             (after_up_pdb_alignment.pdbID != 'nan') & (after_up_pdb_alignment.mutationPositionOnPDB == 'nan')]
         no_pdb = no_pdb.copy()
-  
+        
+        print('-----PDB ALIGNED-----')
+        print(pdb_aligned.to_string())
+        
         print('PDB matching is completed...\n')
         print('SUMMARY')
         print('-------')
@@ -875,6 +890,7 @@ def pdb(input_set, mode, impute):
                 if protein not in existing_modbase_models:
                     print('Downloading Modbase models for ', protein)
                     url = 'https://salilab.org/modbase/retrieve/modbase/?databaseID=' + protein
+                    print(url)
                     req = requests.get(url)
                     name = path_to_output_files / 'modbase_structures' / f'{protein}.txt'
                     with open(name, 'wb') as f:
@@ -1371,6 +1387,7 @@ def pdb(input_set, mode, impute):
 
         aligner = Align.PairwiseAligner()
         print('Proceeding to 3D distance calculation...\n')
+        print(data.to_string())
         data.domainEndonPDB = data.domainEndonPDB.astype(str)
         data.domainStartonPDB = data.domainStartonPDB.astype(str)