pdb_validate outputs to sys.stdout (haddocking#44)

* changed stderr to stdout in validation function

* changed tests

pdbtools/pdb_validate.py

@@ -117,23 +117,23 @@ def _make_pointer(column):
             linelen = len(line)
             if linelen < 80:
                 emsg = '[!] Line {0} is short: {1} < 80\n'
-                sys.stderr.write(emsg.format(iline, linelen))
+                sys.stdout.write(emsg.format(iline, linelen))
                 has_error = True
 
             elif linelen > 80:
                 emsg = '[!] Line {0} is long: {1} > 80\n'
-                sys.stderr.write(emsg.format(iline, linelen))
+                sys.stdout.write(emsg.format(iline, linelen))
                 has_error = True
 
             for fname, (fcol, fcheck) in _fmt_check:
                 field = line[fcol]
                 if not fcheck.match(field):
                     pointer = _make_pointer(fcol)
                     emsg = '[!] Offending field ({0}) at line {1}\n'
-                    sys.stderr.write(emsg.format(fname, iline))
+                    sys.stdout.write(emsg.format(fname, iline))
 
-                    sys.stderr.write(repr(line) + '\n')
-                    sys.stderr.write(pointer + '\n')
+                    sys.stdout.write(repr(line) + '\n')
+                    sys.stdout.write(pointer + '\n')
 
                     has_error = True
                     break
@@ -142,17 +142,17 @@ def _make_pointer(column):
             linelen = len(line)
             if linelen < 80:
                 emsg = '[!] Line {0} is short: {1} < 80\n'
-                sys.stderr.write(emsg.format(iline, linelen))
+                sys.stdout.write(emsg.format(iline, linelen))
                 has_error = True
             elif linelen > 80:
                 emsg = '[!] Line {0} is long: {1} > 80\n'
-                sys.stderr.write(emsg.format(iline, linelen))
+                sys.stdout.write(emsg.format(iline, linelen))
                 has_error = True
 
     if has_error:
         msg = '\nTo understand your errors, read the format specification:\n'
         msg += '  http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\n'
-        sys.stderr.write(msg)
+        sys.stdout.write(msg)
         return 1
     else:
         msg = 'It *seems* everything is OK.'

tests/test_pdb_validate.py

@@ -64,14 +64,14 @@ def test_warnings(self):
 
         # Validate results
         self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(len(self.stderr), 253)
+        self.assertEqual(len(self.stdout), 253)
+        self.assertEqual(len(self.stderr), 0)
 
         # Count no. of line length warnings
-        n_warn = len([l for l in self.stderr if 'is short' in l])
+        n_warn = len([l for l in self.stdout if 'is short' in l])
         self.assertEqual(n_warn, 70)
 
-        self.assertEqual(self.stderr[-4],
+        self.assertEqual(self.stdout[-4],
                          "[!] Line 203 is short: 26 < 80")
 
     def test_valid(self):
@@ -85,8 +85,8 @@ def test_valid(self):
 
         # Validate results
         self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 1)
-        self.assertEqual(len(self.stderr), 0)  # no errors
+        self.assertEqual(len(self.stderr), 0)
+        self.assertEqual(len(self.stdout), 1)  # no errors
 
         self.assertEqual(self.stdout,
                          ["It *seems* everything is OK."])