Move more SFF tests to test_SffIO.py

Bio/SeqIO/SffIO.py

@@ -1311,47 +1311,10 @@ def write_record(self, record):
     with open(filename, "rb") as handle:
         metadata = ReadRocheXmlManifest(handle)
 
-    from Bio._py3k import StringIO
     from io import BytesIO
 
     with open(filename, "rb") as handle:
         sff = list(SffIterator(handle))
-
-    with open("../../Tests/Roche/E3MFGYR02_alt_index_at_end.sff", "rb") as handle:
-        sff2 = list(SffIterator(handle))
-    assert len(sff) == len(sff2)
-    for old, new in zip(sff, sff2):
-        assert old.id == new.id
-        assert str(old.seq) == str(new.seq)
-
-    with open("../../Tests/Roche/E3MFGYR02_alt_index_at_start.sff", "rb") as handle:
-        sff2 = list(SffIterator(handle))
-    assert len(sff) == len(sff2)
-    for old, new in zip(sff, sff2):
-        assert old.id == new.id
-        assert str(old.seq) == str(new.seq)
-
-    with open("../../Tests/Roche/E3MFGYR02_alt_index_in_middle.sff", "rb") as handle:
-        sff2 = list(SffIterator(handle))
-    assert len(sff) == len(sff2)
-    for old, new in zip(sff, sff2):
-        assert old.id == new.id
-        assert str(old.seq) == str(new.seq)
-
-    with open("../../Tests/Roche/E3MFGYR02_index_at_start.sff", "rb") as handle:
-        sff2 = list(SffIterator(handle))
-    assert len(sff) == len(sff2)
-    for old, new in zip(sff, sff2):
-        assert old.id == new.id
-        assert str(old.seq) == str(new.seq)
-
-    with open("../../Tests/Roche/E3MFGYR02_index_in_middle.sff", "rb") as handle:
-        sff2 = list(SffIterator(handle))
-    assert len(sff) == len(sff2)
-    for old, new in zip(sff, sff2):
-        assert old.id == new.id
-        assert str(old.seq) == str(new.seq)
-
     with open(filename, "rb") as handle:
         sff_trim = list(SffIterator(handle, trim=True))
 

Tests/test_SffIO.py

@@ -4,6 +4,7 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
+import sys
 import re
 import unittest
 from io import BytesIO
@@ -263,6 +264,50 @@ def test_both_ways(self):
                 self.assertEqual(len(index1), len(list(SffIterator(BytesIO(handle.read())))))
 
 
+class TestAlternativeIndexes(unittest.TestCase):
+    filename = "Roche/E3MFGYR02_random_10_reads.sff"
+    with open(filename, "rb") as handle:
+        sff = list(SffIterator(handle))
+
+    def check_same(self, new_sff):
+        self.assertEqual(len(self.sff), len(new_sff))
+        for old, new in zip(self.sff, new_sff):
+            self.assertEqual(old.id, new.id)
+            self.assertEqual(str(old.seq), str(new.seq))
+
+    def test_alt_index_at_end(self):
+        with open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb") as handle:
+            sff2 = list(SffIterator(handle))
+        self.check_same(sff2)
+
+    def test_alt_index_at_start(self):
+        with open("Roche/E3MFGYR02_alt_index_at_start.sff", "rb") as handle:
+            sff2 = list(SffIterator(handle))
+        self.check_same(sff2)
+
+    def test_alt_index_in_middle(self):
+        with open("Roche/E3MFGYR02_alt_index_in_middle.sff", "rb") as handle:
+            sff2 = list(SffIterator(handle))
+        self.check_same(sff2)
+
+    def test_index_at_start(self):
+        with open("Roche/E3MFGYR02_index_at_start.sff", "rb") as handle:
+            sff2 = list(SffIterator(handle))
+        self.check_same(sff2)
+
+    def test_index_in_middle(self):
+        with open("Roche/E3MFGYR02_index_in_middle.sff", "rb") as handle:
+            sff2 = list(SffIterator(handle))
+        self.check_same(sff2)
+
+    def test_trim(self):
+        with open(self.filename, "rb") as handle:
+            sff_trim = list(SffIterator(handle, trim=True))
+        self.assertEqual(len(self.sff), len(sff_trim))
+        for old, new in zip(self.sff, sff_trim):
+            self.assertEqual(old.id, new.id)
+
+
 class TestConcatenated(unittest.TestCase):
     def test_parses_gzipped_stream(self):
         import gzip