Addressing biocore#77

CHANGELOG.md

@@ -1,5 +1,11 @@
 # gneiss changelog
 
+## Version 0.2.0
+
+### Features
+* Added filehandle support for write and read io in RegressionResults object [#72](https://github.com/biocore/gneiss/issues/77)
+
+
 ## Version 0.1.3
 
 ### Features

gneiss/regression/_summary.py

@@ -271,7 +271,7 @@ def read_pickle(self, filename):
 
         Parameters
         ----------
-        filename : str
+        filename : str or filehandle
             Input file to unpickle.
 
         Returns
@@ -283,18 +283,23 @@ def read_pickle(self, filename):
         Warning: Loading pickled data received from untrusted
         sources can be unsafe. See: https://wiki.python.org/moin/UsingPickle
         """
-        with open(filename, 'rb') as fh:
-            res = pickle.load(fh)
+        if isinstance(filename, str):
+            with open(filename, 'rb') as fh:
+                res = pickle.load(fh)
+        else:
+            res = pickle.load(filename)
         return res
 
     def write_pickle(self, filename):
         """ Writes RegressionResults object to pickle file.
 
         Parameters
         ----------
-        filename : str
+        filename : str or filehandle
             Output file to store pickled object.
         """
-
-        with open(filename, 'wb') as fh:
-            pickle.dump(self, fh)
+        if isinstance(filename, str):
+            with open(filename, 'wb') as fh:
+                pickle.dump(self, fh)
+        else:
+            pickle.dump(self, filename)

gneiss/regression/tests/test_summary.py

@@ -225,6 +225,17 @@ def test_read_write(self):
         self.assertEqual(str(res.tree), str(exp.tree))
         pdt.assert_frame_equal(res.pvalues, exp.pvalues)
 
+    def test_read_write_handle(self):
+        fh = open(self.pickle_fname, 'wb')
+        exp = RegressionResults(self.results, tree=self.tree)
+        exp.write_pickle(fh)
+        fh.close()
+        fh = open(self.pickle_fname, 'rb')
+        res = RegressionResults.read_pickle(self.pickle_fname)
+        fh.close()
+        self.assertEqual(str(res.tree), str(exp.tree))
+        pdt.assert_frame_equal(res.pvalues, exp.pvalues)
+
 
 if __name__ == "__main__":
     unittest.main()