{AH} add unit tests to check return type for string/byte output, closes #292

Author: AndreasHeger

pysam/cutils.pyx

@@ -297,7 +297,6 @@ def _pysam_dispatch(collection,
     # setup the function call to samtools/bcftools main
     cdef char ** cargs
     cdef int i, n, retval, l
-
     n = len(args)
     method = force_bytes(method)
     collection = force_bytes(collection)

pysam/utils.py

@@ -71,8 +71,8 @@ def __call__(self, *args, **kwargs):
                 "stdout=%s, stderr=%s" %
                 (self.collection,
                  retval, 
-                 "\n".join(stdout),
-                 "\n".join(stderr)))
+                 stdout,
+                 stderr))
 
         self.stderr = stderr
 

tests/samtools_test.py

@@ -243,6 +243,28 @@ def testEmptyIndex(self):
         self.assertRaises(IOError, pysam.samtools.index,
                           "exdoesntexist.bam")
 
+class TestReturnType(unittest.TestCase):
+    
+    def testReturnValueString(self):
+        retval = pysam.idxstats(os.path.join(DATADIR, "ex1.bam"))
+        if IS_PYTHON3:
+            self.assertFalse(isinstance(retval, bytes))
+            self.assertTrue(isinstance(retval, str))
+        else:
+            self.assertTrue(isinstance(retval, bytes))
+            self.assertTrue(isinstance(retval, basestring))
+
+    def testReturnValueData(self):
+        args = "-O BAM {}".format(os.path.join(DATADIR, "ex1.bam")).split(" ")
+        retval = pysam.view(*args)
+
+        if IS_PYTHON3:
+            self.assertTrue(isinstance(retval, bytes))
+            self.assertFalse(isinstance(retval, str))
+        else:
+            self.assertTrue(isinstance(retval, bytes))
+            self.assertTrue(isinstance(retval, basestring))
+
 
 class StdoutTest(unittest.TestCase):
     '''test if stdout can be redirected.'''