Raise StopIteration (not return None) in Bio.AlignIO (Bug 3147)

Bio/AlignIO/ClustalIO.py

@@ -91,7 +91,7 @@ def next(self):
         except AttributeError:      
             line = handle.readline()
         if not line:
-            return None
+            raise StopIteration
 
         #Whitelisted headers we know about
         known_headers = ['CLUSTAL', 'PROBCONS', 'MUSCLE']
@@ -245,7 +245,7 @@ def next(self):
 
         assert len(ids) == len(seqs)
         if len(seqs) == 0 or len(seqs[0]) == 0:
-            return None
+            raise StopIteration
 
         if self.records_per_alignment is not None \
         and self.records_per_alignment != len(ids):

Bio/AlignIO/EmbossIO.py

@@ -76,12 +76,12 @@ def next(self):
         except AttributeError:      
             line = handle.readline()
         if not line:
-            return None
+            raise StopIteration
 
         while line.rstrip() != "#=======================================":
             line = handle.readline()
             if not line:
-                return None
+                raise StopIteration
 
         length_of_seqs = None
         number_of_seqs = None

Bio/AlignIO/FastaIO.py

@@ -76,7 +76,7 @@ def next(self):
         except AttributeError:      
             line = handle.readline()
         if not line:
-            return None
+            raise StopIteration
 
         if line.startswith("#"):
             #Skip the file header before the alignments.  e.g.
@@ -90,10 +90,10 @@ def next(self):
             #Now should be some alignments, but if not we move onto the next query
         if not line:
             #End of file
-            return None
+            raise StopIteration
         if ">>><<<" in line:
             #Reached the end of the alignments, no need to read the footer...
-            return None
+            raise StopIteration
 
 
         #Should start >>... and not >>>...

Bio/AlignIO/PhylipIO.py

@@ -145,7 +145,8 @@ def next(self):
         except AttributeError:
             line = handle.readline()
 
-        if not line: return
+        if not line:
+            raise StopIteration
         line = line.strip()
         parts = filter(None, line.split())
         if len(parts)!=2:

Bio/AlignIO/StockholmIO.py

@@ -318,7 +318,7 @@ def next(self):
             line = self.handle.readline()
         if not line:
             #Empty file - just give up.
-            return
+            raise StopIteration
         if not line.strip() == '# STOCKHOLM 1.0':
             raise ValueError("Did not find STOCKHOLM header")
             #import sys
@@ -453,7 +453,7 @@ def next(self):
 
             return alignment
         else:
-            return None
+            raise StopIteration
 
 
     def _identifier_split(self, identifier):

Bio/AlignIO/__init__.py

@@ -269,9 +269,7 @@ def _SeqIO_to_alignment_iterator(handle, format, alphabet=None, seq_count=None):
         records = list(SeqIO.parse(handle, format, alphabet))
         if records:
             yield MultipleSeqAlignment(records, alphabet)
-        else:
-            #No alignment found!
-            pass
+    raise StopIteration
 
 def _force_alphabet(alignment_iterator, alphabet):
     """Iterate over alignments, over-riding the alphabet (PRIVATE)."""

Tests/test_AlignIO.py

@@ -238,11 +238,9 @@ def simple_alignment_comparison(alignments, alignments2, format):
         try:
             record = seq_iterator.next()
         except StopIteration:
-            record = None
-        if record:
-            alignments3.append(record)
-        else:
             break
+        assert record is not None, "Should raise StopIteration not return None"
+        alignments3.append(record)
 
     #Try a mixture of next() and list (a torture test!)
     seq_iterator = AlignIO.parse(handle=open(t_filename,"r"), format=t_format)