[Biopython-dev] [Biopython - Bug #3268] (New) Windows and Python 3 specific unicode problem in SeqIO / SeqXML

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Fri Jul 22 17:43:49 UTC 2011

Issue #3268 has been reported by Peter Cock.

Bug #3268: Windows and Python 3 specific unicode problem in SeqIO / SeqXML

Author: Peter Cock
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 

We're seeing unittest failures under Python 3.1 and 3.2 on Windows XP via the buildbot,


FAIL: test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Test special unicode characters in the description.
Traceback (most recent call last):
  File "c:\repositories\BuildBot\win31\build\build\py3.1\Tests\test_SeqIO_SeqXML.py", line 55, in test_unicode_characters_desc
    self.assertEqual(self.records["rna"][2].description, "\u00E5\u00C5\u00FC\u00F6\u00D6\u00DF\u00F8\u00E4\u00A2\u00A3$\u20AC\u9999\u80A0")
AssertionError: 'åÅüöÖßø䢣$€香�\xa0' != '�������䢣$�\u9999\u80a0'


This test is currently working on Linux, Mac OS X for Python 3.

There was a similar failure in Jython 2.5.1 (cross platform), now fixed in Jython 2.5.2, see:


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