Merge pull request #620 from pysam-developers/AH-add_alignmentfilehea…

…der_dict_methods

{AH} add backwards compatibility functions for AlignmentHeader, fixes…

pysam/libcalignmentfile.pyx

@@ -531,6 +531,35 @@ cdef class AlignmentHeader(object):
             text += "\n" + self._build_sequence_section()
         return text
 
+    # dictionary access methods, for backwards compatibility.
+    def __setitem__(self, key, value):
+        raise TypeError("AlignmentHeader does not support item assignment (use header.to_dict()")
+
+    def __getitem__(self, key):
+        return self.to_dict().__getitem__(key)
+
+    def items(self):
+        return self.to_dict().items()
+
+    # PY2 compatibility
+    def iteritems(self):
+        return self.to_dict().items()
+
+    def keys(self):
+        return self.to_dict().keys()
+
+    def values(self):
+        return self.to_dict().values()
+
+    def get(self, *args):
+        return self.to_dict().get(*args)
+
+    def __len__(self):
+        return self.to_dict().__len__()
+
+    def __contains__(self, key):
+        return self.to_dict().__contains__(key)
+
 
 cdef class AlignmentFile(HTSFile):
     """AlignmentFile(filepath_or_object, mode=None, template=None,

tests/AlignmentFileHeader_test.py

@@ -173,6 +173,37 @@ def test_name_mapping(self):
         self.assertEqual(self.samfile.gettid("chr?"), -1)
         self.assertRaises(ValueError, self.samfile.getrname, 2)
 
+    def test_dictionary_access_works(self):
+        for key in self.header.keys():
+            self.compare_headers({key: self.header[key]},
+                                 {key: self.samfile.header[key]})
+
+    def test_dictionary_setting_raises_error(self):
+        self.assertRaises(TypeError,
+                          self.samfile.header.__setitem__,
+                          "CO",
+                          ["This is a final comment"])
+
+    def test_dictionary_len_works(self):
+        self.assertEqual(len(self.header), len(self.samfile.header))
+
+    def test_dictionary_keys_works(self):
+        # sort for py2.7
+        self.assertEqual(sorted(self.header.keys()),
+                         sorted(self.samfile.header.keys()))
+
+    def test_dictionary_values_works(self):
+        self.assertEqual(len(self.header.values()), len(self.samfile.header.values()))
+
+    def test_dictionary_get_works(self):
+        self.assertEqual(self.header.get("HD"), {'VN': '1.0'})
+        self.assertEqual(self.header.get("UK", "xyz"), "xyz")
+        self.assertEqual(self.header.get("UK"), None)
+
+    def test_dictionary_contains_works(self):
+        self.assertTrue("HD" in self.header)
+        self.assertFalse("UK" in self.header)
+
     def tearDown(self):
         self.samfile.close()