[Biopython-dev] [Bug 3042] New: test_Mafft_tool fails

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3042

           Summary: test_Mafft_tool fails
           Product: Biopython
           Version: 1.54b
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mdehoon at ims.u-tokyo.ac.jp


This is the error message I get:

======================================================================
FAIL: Simple round-trip through app with infile.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Mafft_tool.py", line 56, in test_Mafft_simple
    self.assert_("STEP     2 / 2 d" in stderr_string)
AssertionError

======================================================================
FAIL: Round-trip with complex command line.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Mafft_tool.py", line 126, in test_Mafft_with_complex_command_line
    self.assertEqual(return_code, 0)
AssertionError: 1 != 0


This is with MAFFT version 5.732 (2005/09/14). The output it generates starts
with:

$ mafft Fasta/f002
blosum 62
ppenalty = -1530
poffset = -123
generating 200PAM scoring matrix for nucleotides ... done
scoremtx = -1
Gap Penalty = -1.53, +0.00, -0.12

Making a distance matrix ..
   1 /    3nknown character n
done.

Constructing dendrogram ...
0 / 3
done.

Progressive alignment ...
STEP 2 /2
done.



Whereas the bug may disappear with newer versions of mafft, most Biopython
users will not use mafft, and we should not require to have the latest version
of mafft installed to avoid test errors.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.