scripts/pdbfilter.py does not filter out the same protein for some cases.

[huhlim]

:exclamation: Make to check out our User Guide.

Expected Behavior

When a PDB has multiple chains of the same protein, I expect the script to leave only one of the chains. For example with the following input files,

• cluster.tsv

  4APC_A  4APC_A
  4APC_A  4APC_B
  4APC_A  4B9D_A
  4APC_A  4B9D_B

• pdb_filter.dat

  #pdb_chain  resolution  r_free  completeness    method
  4APC_A  2.1 0.248   0.837   X-RAY DIFFRACTION
  4APC_B  2.1 0.248   0.846   X-RAY DIFFRACTION
  4B9D_A  1.9 0.222   0.829   X-RAY DIFFRACTION
  4B9D_B  1.9 0.222   0.843   X-RAY DIFFRACTION

  I expected it resulted in one representative output, but it resulted in two sequences, 4B9D_B and 4APC_B.

  Current Behavior

  It occasionally resulted in multiple chains.

  Steps to Reproduce (for bugs)

  pdbfilter_debug.zip

  unzip pdbfilter_debug.zip
  cd pdbfilter_debug
  pdbfilter.py input.fas cluster.tsv pdb_filter.dat output.fas

  Suggested debugging

  As they are in the same cluster, I think they should result in one representative sequence. I think it can be debugged by modifying the file like this:

      if best_entry_res is not None:
          selected_sequences.add(best_entry_res)
  
          if DEBUG:
              print (' - Selected {n} (best resolution = {r}).'.format(
                  n = best_entry_res,
                  r = best_res))
  
      elif best_entry_rfr is not None:
          selected_sequences.add(best_entry_rfr)
  
          if DEBUG:
              print (' - Selected {n} (best R-free = {r}).'.format(
                  n = best_entry_rfr,
                  r = best_rfr))
  
      elif best_entry_comp is not None:
          selected_sequences.add(best_entry_comp)
  
          if DEBUG:
              print (' - Selected {n} (best completness = {r}).'.format(
                  n = best_entry_comp,
                  r = best_comp))    
  
      else best_entry_res == None and best_entry_rfr == None and best_entry_comp == None:
          print ('! Warning: Did not find any representative entry for cluster {c}.'.format(
              c = cluster))