[Biopython-dev] [Bug 3042] test_Mafft_tool fails

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

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





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2010-05-06 13:08 EST -------
(In reply to comment #0)
> 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

I have changed that to look for "Progressive alignment ..." instead
which is present in both this MAFFT 5.x output and in MAFFT 6.x output.

> ======================================================================
> 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

I've changed this to give the command line used to help debug when MAFFT
returns an error code. Could you retest and report what MAFFT does for
this particular command?

Also what is the output of "mafft --help" from MAFFT 5.732? That would be
useful if we do have to make running the test conditional on the version of
MAFFT.

Thanks!


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