{AH} fix py3 StringIO issues

Author: AndreasHeger

pysam/calignmentfile.pyx

@@ -57,7 +57,6 @@ import collections
 import re
 import warnings
 import array
-import StringIO
 
 from cpython cimport array as c_array
 from cpython.version cimport PY_MAJOR_VERSION
@@ -67,6 +66,11 @@ from pysam.cutils cimport encode_filename, from_string_and_size
 from pysam.calignedsegment cimport makeAlignedSegment, makePileupColumn
 from pysam.chtslib cimport hisremote
 
+if PY_MAJOR_VERSION >= 3:
+    from io import StringIO
+else:
+    from StringIO import StringIO
+
 cimport cython
 
 ########################################################
@@ -408,17 +412,18 @@ cdef class AlignmentFile:
         if self.htsfile != NULL:
             self.close()
 
-        # check if we are working with a File object
-        if hasattr(filepath_or_object, "fileno"):
-            filename = filepath_or_object.name
-            if filepath_or_object.closed:
-                raise ValueError('I/O operation on closed file')
-        elif isinstance(filepath_or_object, StringIO.StringIO):
+        # StringIO not supported
+        if isinstance(filepath_or_object, StringIO):
             filename = "stringio"
             raise NotImplementedError(
                 "access from StringIO objects not supported")
             if filepath_or_object.closed:
                 raise ValueError('I/O operation on closed StringIO object')
+        # check if we are working with a File object
+        elif hasattr(filepath_or_object, "fileno"):
+            filename = filepath_or_object.name
+            if filepath_or_object.closed:
+                raise ValueError('I/O operation on closed file')
         else:
             filename = filepath_or_object
 

tests/AlignmentFile_test.py

@@ -13,7 +13,11 @@
 import subprocess
 import logging
 import array
-import StringIO
+if sys.version_info.major >= 3:
+    from io import StringIO
+else:
+    from StringIO import StringIO
+
 from functools import partial
 
 import pysam
@@ -375,8 +379,11 @@ def testRaises(self):
         statement = "samtools view -h {}".format(
                 os.path.join(DATADIR, "ex3.bam"))
         stdout = subprocess.check_output(statement.split(" "))
-        bam = StringIO.StringIO()
-        bam.write(stdout)
+        bam = StringIO()
+        if sys.version_info.major >= 3:
+            bam.write(stdout.decode('ascii'))
+        else:
+            bam.write(stdout)
         bam.seek(0)
         self.assertRaises(NotImplementedError,
                           pysam.AlignmentFile, bam)