update PAML yn00 tests to handle new test resource directory structure

Tests/test_PAML_yn00.py

@@ -11,14 +11,19 @@
 
 class ModTest(unittest.TestCase):
 
-    align_file = os.path.join("PAML", "alignment.phylip")
-    out_file = os.path.join("PAML", "test.out")
+    align_dir = os.path.join("PAML", "Alignments")
+    tree_dir = os.path.join("PAML", "Trees")
+    ctl_dir = os.path.join("PAML", "Control_files")
+    results_dir = os.path.join("PAML", "Results")
     working_dir = os.path.join("PAML", "yn00_test")
-    results_file = os.path.join("PAML", "bad_results.out")
-    bad_ctl_file1 = os.path.join("PAML", "bad1.ctl")
-    bad_ctl_file2 = os.path.join("PAML", "bad2.ctl")
-    ctl_file = os.path.join("PAML", "yn00.ctl")
-
+
+    align_file = os.path.join(align_dir, "alignment.phylip")
+    out_file = os.path.join(results_dir, "test.out")
+    results_file = os.path.join(results_dir, "bad_results.out")
+    bad_ctl_file1 = os.path.join(ctl_dir, "bad1.ctl")
+    bad_ctl_file2 = os.path.join(ctl_dir, "bad2.ctl")
+    ctl_file = os.path.join(ctl_dir, "yn00", "yn00.ctl")
+
     def __del__(self):
         """Just in case yn00 creates some junk files, do a clean-up."""
         del_files = [self.out_file, "2YN.dN", "2YN.dS", "2YN.t", "rst",
@@ -127,15 +132,14 @@ def testResultsParsable(self):
         self.assertRaises(ValueError, yn00.read, self.results_file)
 
     def testParseAllVersions(self):
-        folder = os.path.join("PAML","Results", "yn00", "versions")
+        folder = os.path.join(self.results_dir, "yn00")
         for results_file in os.listdir(folder):
             file_path = os.path.join(folder, results_file)
-            if os.path.isfile(file_path) and results_file[:4] == "yn00":
-                results = yn00.read(file_path)
-                self.assertEqual(len(results), 5)
-                self.assertEqual(len(results["Homo_sapie"]), 4)
-                self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]),
-                    5)
+            results = yn00.read(file_path)
+            self.assertEqual(len(results), 5)
+            self.assertEqual(len(results["Homo_sapie"]), 4)
+            self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]),
+                5)
 
 if __name__ == "__main__":
     runner = unittest.TextTestRunner(verbosity = 2)