Test the GckIO module against an artificial sample.

Ensure the Bio.SeqIO.GckIO module can be tested even in offline
mode by reading an in-tree artificial sample file.

This sample file has been handcrafted based on what I know about
the Gck format, solely for the purpose of testing the parser. It
is not even sure the original Gene Construction Kit program would
accept that file without barking.

Testing the parser against real files is still recommended. The
test module will still do that automatically using files from the
Drosophila Gateway Vector Collection provided those files can be
downloaded.

Tests/Gck/README

@@ -1,2 +0,0 @@
-This directory is intended for sample Gck files which will be
-automatically downloaded when running the tests suite.

Tests/test_SeqIO_Gck.py

@@ -288,9 +288,6 @@ class TestGckWithDGVC(unittest.TestCase):
                 return
 
         self.zipdata = ZipFile('Gck/DGVC_GCK.zip')
-        with self.zipdata.open('Drosophila Gateway Vectors GCK/pACW') as f:
-            # Keep one of the file in memory for the corruption tests below
-            self.buffer = f.read()
 
     def tearDown(self):
         self.zipdata.close()
@@ -318,6 +315,36 @@ class TestGckWithDGVC(unittest.TestCase):
 
             f.close()
 
+
+class TestGckWithArtificialData(unittest.TestCase):
+
+    def setUp(self):
+        with open('Gck/artificial.gck', 'rb') as f:
+            self.buffer = f.read()
+
+    def test_read(self):
+        """Read an artificial sample file."""
+        h = BytesIO(self.buffer)
+        record = SeqIO.read(h, 'gck')
+        self.assertEqual('ACGTACGTACGT', record.seq)
+        self.assertEqual('Sample construct', record.description)
+        self.assertEqual('linear', record.annotations['topology'])
+        self.assertEqual(2, len(record.features))
+
+        self.assertEqual(2, record.features[0].location.start)
+        self.assertEqual(6, record.features[0].location.end)
+        self.assertEqual(1, record.features[0].location.strand)
+        self.assertEqual('misc_feature', record.features[0].type)
+        self.assertEqual('FeatureA', record.features[0].qualifiers['label'][0])
+
+        self.assertEqual(7, record.features[1].location.start)
+        self.assertEqual(11, record.features[1].location.end)
+        self.assertEqual(-1, record.features[1].location.strand)
+        self.assertEqual('CDS', record.features[1].type)
+        self.assertEqual('FeatureB', record.features[1].qualifiers['label'][0])
+
+        h.close()
+
     def munge_buffer(self, position, value):
         mod_buffer = bytearray(self.buffer)
         if isinstance(value, list):
@@ -329,25 +356,25 @@ class TestGckWithDGVC(unittest.TestCase):
     def test_conflicting_lengths(self):
         """Read a file with incorrect length."""
         # Change the sequence length as indicated in the sequence packet
-        h = self.munge_buffer(28, [0x00, 0x00, 0x20, 0x15])
+        h = self.munge_buffer(0x1C, [0x00, 0x00, 0x20, 0x15])
         with self.assertRaisesRegexp(ValueError, "Conflicting sequence length values"):
             SeqIO.read(h, 'gck')
         h.close()
 
         # Change the sequence length as indicated in the features packet
-        h = self.munge_buffer(8135, [0x00, 0x00, 0x20, 0x15])
+        h = self.munge_buffer(0x36, [0x00, 0x00, 0x20, 0x15])
         with self.assertRaisesRegexp(ValueError, "Conflicting sequence length values"):
             SeqIO.read(h, 'gck')
         h.close()
 
         # Change the number of features
-        h = self.munge_buffer(8140, 0x30)
+        h = self.munge_buffer(0x3B, 0x30)
         with self.assertRaisesRegexp(ValueError, "Features packet size inconsistent with number of features"):
             SeqIO.read(h, 'gck')
         h.close()
 
         # Change the number of restriction sites
-        h = self.munge_buffer(10528, 0x30)
+        h = self.munge_buffer(0x137, 0x30)
         with self.assertRaisesRegexp(ValueError, "Sites packet size inconsistent with number of sites"):
             SeqIO.read(h, 'gck')
         h.close()