Use the warnings module rather than printing/writing to stdout and st…

…derr. Based on ideas from Eric Talevich (Bug 2754)

Bio/PDB/Dice.py

@@ -4,7 +4,7 @@
 # as part of this package.
 
 import re
-
+import warnings
 from Bio.PDB.PDBIO import PDBIO
 
 
@@ -41,7 +41,8 @@ def accept_residue(self, residue):
             # skip HETATMS
             return 0
         if icode!=" ":
-            print "WARNING: Icode at ", residue.get_id()
+            warnings.warn("WARNING: Icode at %s" % residue.get_id(),
+                          RuntimeError)
         if self.start<=resseq<=self.end:
             return 1
         return 0

Bio/PDB/HSExposure.py

@@ -4,7 +4,7 @@
 # as part of this package.
 
 from math import pi
-import sys
+import warnings
 
 from Bio.PDB import *
 from AbstractPropertyMap import AbstractPropertyMap
@@ -201,7 +201,7 @@ def pcb_vectors_pymol(self, filename="hs_exp.py"):
         @type filename: string
         """
         if len(self.ca_cb_list)==0:
-            sys.stderr.write("Nothing to draw.\n")
+            warnings.warn("Nothing to draw.", RuntimeWarning)
             return
         fp=open(filename, "w")
         fp.write("from pymol.cgo import *\n")

Bio/PDB/MMCIF2Dict.py

@@ -76,7 +76,8 @@ def _make_mmcif_dict(self):
                         token, value=get_token()  
                         # print token, value
                     if pos!=nr_fields-1:
-                        print "ERROR: broken name-data pair (data missing)!"
+                        warnings.warn("ERROR: broken name-data pair "
+                                      "(data missing)!", RuntimeError)
                     # The last token was not used, so
                     # don't set token to None! (this means the 
                     # last parsed token goes through the loop again)
@@ -87,7 +88,8 @@ def _make_mmcif_dict(self):
                     # print token, value
                     mmcif_dict[value]=data
                     if next_token<4:
-                        print "ERROR: broken name-data pair (name-non data pair)!"  
+                        warnings.warn("ERROR: broken name-data pair "
+                                      "(name-non data pair)!", RuntimeError)
                         # print token, value
                     else:   
                         # get next token
@@ -102,8 +104,9 @@ def _make_mmcif_dict(self):
                 token=None
             else:
                 # we found some complete garbage
-                print "ERROR: broken name-data pair (missing name)!"
-                print token, value
+                warnings.warn("ERROR: broken name-data pair "
+                              "(missing name)!\n%s %s" % (token, value),
+                              RuntimeError)
                 mmcif_dict[None].append(value)
                 # get next token
                 token=None

Bio/PDB/PDBList.py

@@ -35,7 +35,8 @@
 
 __doc__="Access the PDB over the internet (for example to download structures)."
 
-import urllib, re, os, sys
+import urllib, re, os
+from warnings import warn
 
 class PDBList:
     """
@@ -147,7 +148,7 @@ def get_all_entries(self):
         Returns a list of PDB codes in the index file.
         """
         entries = []
-        print "retrieving index file. Takes about 5 MB."
+        warnings.warn("retrieving index file. Takes about 5 MB.")
         url = urllib.urlopen(self.pdb_server+'/pub/pdb/derived_data/index/entries.idx')
         # extract four-letter-codes
         entries = map(lambda x: x[:4], \
@@ -232,11 +233,12 @@ def retrieve_pdb_file(self,pdb_code, obsolete=0, compression='.gz',
         # check whether the file exists
         if not self.overwrite:
             if os.path.exists(final_file):
-                print "file exists, not retrieved",final_file
+                warnings.warn("file exists, not retrieved %s" % final_file,
+                              RuntimeError)
                 return final_file
 
         # Retrieve the file
-        print 'retrieving',url                    
+        warnings.warn('retrieving %s' % url)
         lines=urllib.urlopen(url).read()
         open(filename,'wb').write(lines)
         # uncompress the file
@@ -260,10 +262,10 @@ def update_pdb(self):
 
         for pdb_code in new+modified:
             try:
-                print 'retrieving %s'%(pdb_code)            
+                warnings.warn('retrieving %s' % pdb_code)
                 self.retrieve_pdb_file(pdb_code)
             except:
-                print 'error %s'%(pdb_code)
+                warnings.warn('error %s' % pdb_code, RuntimeError)
                 # you can insert here some more log notes that
                 # something has gone wrong.            
 
@@ -311,14 +313,17 @@ def download_obsolete_entries(self,listfile=None):
     def get_seqres_file(self,savefile='pdb_seqres.txt'):
         """Retrieves a (big) file containing all the sequences 
         of PDB entries and writes it to a file."""
-        print "retrieving sequence file. Takes about 15 MB."
+        warnings.warn("retrieving sequence file. Takes about 15 MB.")
         url = urllib.urlopen(self.pdb_server+'/pub/pdb/derived_data/pdb_seqres.txt')        
         file = url.readlines()
         open(savefile,'w').writelines(file)
 
 
 
 if __name__ == '__main__':
+
+    import sys
+
     doc = """PDBList.py
     (c) Kristian Rother 2003, Contributed to BioPython
 
@@ -367,7 +372,4 @@ def get_seqres_file(self,savefile='pdb_seqres.txt'):
         elif re.search('^\d...$',sys.argv[1]):
             # get single PDB entry
             pl.retrieve_pdb_file(sys.argv[1],pdir=pdb_path)
-
-
-
 

Bio/PDB/PDBParser.py

@@ -4,8 +4,7 @@
 # as part of this package.  
 
 # Python stuff
-import sys
-
+import warnings
 import numpy
 
 # My stuff
@@ -242,8 +241,10 @@ def _handle_PDB_exception(self, message, line_counter):
         message="%s at line %i." % (message, line_counter)
         if self.PERMISSIVE:
             # just print a warning - some residues/atoms may be missing
-            print "PDBConstructionException: %s" % message
-            print "Exception ignored.\nSome atoms or residues may be missing in the data structure."
+            warnings.warn("PDBConstructionException: %s\n"
+                          "Exception ignored.\n"
+                          "Some atoms or residues may be missing in the data structure."
+                          % message, RuntimeWarning)
         else:
             # exceptions are fatal - raise again with new message (including line nr)
             raise PDBConstructionException(message)

Bio/PDB/StructureBuilder.py

@@ -3,14 +3,12 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.  
 
-import sys
-
-
 __doc__="""
 Consumer class that builds a Structure object. This is used by 
 the PDBParser and MMCIFparser classes.
 """
 
+import warnings
 
 # My stuff 
 # SMCRA hierarchy
@@ -82,8 +80,9 @@ def init_chain(self, chain_id):
         if self.model.has_id(chain_id):
             self.chain=self.model[chain_id]
             if __debug__:
-                sys.stderr.write("WARNING: Chain %s is discontinuous at line %i.\n" 
-                        % (chain_id, self.line_counter))
+                warnings.warn("WARNING: Chain %s is discontinuous at line %i."
+                              % (chain_id, self.line_counter),
+                              RuntimeWarning)
         else:
             self.chain=Chain(chain_id)
             self.model.add(self.chain)
@@ -117,8 +116,10 @@ def init_residue(self, resname, field, resseq, icode):
                 # There already is a residue with the id (field, resseq, icode).
                 # This only makes sense in the case of a point mutation.
                 if __debug__:
-                    sys.stderr.write("WARNING: Residue ('%s', %i, '%s') redefined at line %i.\n" 
-                            % (field, resseq, icode, self.line_counter))
+                    warnings.warn("WARNING: Residue ('%s', %i, '%s') "
+                                  "redefined at line %i."
+                                  % (field, resseq, icode, self.line_counter),
+                                  RuntimeWarning)
                 duplicate_residue=self.chain[res_id]
                 if duplicate_residue.is_disordered()==2:
                     # The residue in the chain is a DisorderedResidue object.
@@ -187,8 +188,11 @@ def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname, serial_n
                     # name of current atom now includes spaces
                     name=fullname
                     if __debug__:
-                        sys.stderr.write("WARNING: atom names %s and %s differ only in spaces at line %i.\n" 
-                            % (duplicate_fullname, fullname, self.line_counter))
+                        warnings.warn("WARNING: atom names %s and %s differ "
+                                      "only in spaces at line %i."
+                                      % (duplicate_fullname, fullname,
+                                         self.line_counter),
+                                      RuntimeWarning)
         atom=self.atom=Atom(name, coord, b_factor, occupancy, altloc, fullname, serial_number)
         if altloc!=" ":
             # The atom is disordered
@@ -210,8 +214,9 @@ def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname, serial_n
                     disordered_atom.disordered_add(duplicate_atom)
                     residue.flag_disordered()
                     if __debug__:
-                        sys.stderr.write("WARNING: disordered atom found with blank altloc before line %i.\n"  
-                                % self.line_counter)
+                        warnings.warn("WARNING: disordered atom found "
+                                      "with blank altloc before line %i.\n"
+                                      % self.line_counter, RuntimeWarning)
             else:
                 # The residue does not contain this disordered atom
                 # so we create a new one.

Tests/output/test_PDB

@@ -2,9 +2,17 @@ test_PDB
 PDBConstructionException: Atom N defined twice in residue <Residue ARG het=  resseq=2 icode= > at line 19.
 Exception ignored.
 Some atoms or residues may be missing in the data structure.
+WARNING: disordered atom found with blank altloc before line 31.
+
+WARNING: Residue (' ', 4, ' ') redefined at line 41.
 PDBConstructionException: Blank altlocs in duplicate residue SER (' ', 4, ' ') at line 41.
 Exception ignored.
 Some atoms or residues may be missing in the data structure.
+WARNING: Residue (' ', 10, ' ') redefined at line 73.
+WARNING: Residue (' ', 14, ' ') redefined at line 104.
+WARNING: Residue (' ', 16, ' ') redefined at line 133.
+WARNING: Residue (' ', 80, ' ') redefined at line 631.
+WARNING: Residue (' ', 81, ' ') redefined at line 644.
 PDBConstructionException: Atom O defined twice in residue <Residue HOH het=W resseq=67 icode= > at line 820.
 Exception ignored.
 Some atoms or residues may be missing in the data structure.

Tests/test_PDB.py

@@ -10,8 +10,10 @@
     raise MissingExternalDependencyError(\
         "Install NumPy if you want to use Bio.PDB.")
 
-import sys
-# Redirect stderr so user does not see warnings
+import warnings
+def send_warnings_to_stdout(message, category, filename, lineno, file=None):
+    print message
+warnings.showwarning = send_warnings_to_stdout
 
 def quick_neighbor_search_test() :
     #Based on the self test in Bio.PDB.NeighborSearch
@@ -89,12 +91,4 @@ def run_test():
     print "NeighborSearch test"
     quick_neighbor_search_test()
 
-
-
-old_stderr = sys.stderr
-# Hide stderr output for user
-sys.stderr=TheVoid()
-try:
-    run_test()
-finally:
-    sys.stderr = old_stderr
+run_test()