Bio.Motif C code unit test (from Bartek's example on mailing list)

Tests/test_Motif_pwm.py

@@ -0,0 +1,37 @@
+# Copyright 2010 by Bartek Wilczynski.  All rights reserved.
+# Copyright 2010 by Peter Cock.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+import os
+import unittest
+
+from Bio import Seq
+from Bio import Motif
+
+try:
+    from Bio.Motif import _pwm
+except ImportError:
+    #Failed to import the C code extension module
+    from Bio import MissingExternalDependencyError
+    raise MissingExternalDependencyError(\
+        "C module in Bio.Motif not compiled")
+
+class MotifTestsBasic(unittest.TestCase):
+    def test_simple(self):
+        """Test if Motif C code works."""
+        m=Motif.read(open("Motif/SRF.pfm"),"jaspar-pfm")
+        result = m.scanPWM(Seq.Seq("ACGTGTGCGTAGTGCGT",m.alphabet))
+        self.assertEqual(6, len(result))
+        self.assertAlmostEqual(result[0], -29.18363571)
+        self.assertAlmostEqual(result[1], -38.3365097)
+        self.assertAlmostEqual(result[2], -29.17756271)
+        self.assertAlmostEqual(result[3], -38.04542542)
+        self.assertAlmostEqual(result[4], -20.3014183)
+        self.assertAlmostEqual(result[5], -25.18009186)
+
+
+if __name__ == "__main__":
+    runner = unittest.TextTestRunner(verbosity = 2)
+    unittest.main(testRunner=runner)