[Biopython-dev] [Bug 2880] test_Mafft_tool.py unit test failure

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2880


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|Two unit tests issues in    |test_Mafft_tool.py unit test
                   |1.51b (t-coffee and mafft)  |failure




------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2009-07-18 15:35 EST -------
(In reply to comment #4)
> # python run_tests.py test_TCoffee_tool.py
> test_TCoffee_tool ... ok
> ----------------------------------------------------------------------
> Ran 1 test in 3.627 seconds
> 
> # t_coffee
> 
> PROGRAM: T-COFFEE (Version_7.54)
> -full_log       S       [0] 
> ...
> [cut]
> # t_coffee -version
> PROGRAM: T-COFFEE (Version_7.54)

OK - that all looks as I would hope.

> # python run_tests.py test_Mafft_tool.py
> test_Mafft_tool ... FAIL
> ======================================================================
> FAIL: Simple round-trip through app with clustal output
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/var/tmp/portage/sci-biology/biopython-1.51b/work/biopython-1.51b/Tests/test_Mafft_tool.py",
> line 78, in test_Mafft_with_Clustalw_output
>     self.assert_(stdout.read().startswith("CLUSTAL format alignment by MAFFT"))
> AssertionError
> 
> ----------------------------------------------------------------------
> Ran 1 test in 1.598 seconds
> 
> FAILED (failures = 1)
> # python setup.py test
> [cut]
> test_Seq_objs ... ok
> test_SubsMat ... ok
> test_SwissProt ... ok
> test_TCoffee_tool ... ok
> test_UniGene ... ok
> test_UniGene_obsolete ... ok
> test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
> test_align ... ok
> test_geo ... ok
> test_interpro ... ok
> test_kNN ... ok
> test_lowess ... ok
> test_pairwise2 ... ok
> test_prodoc ... ok
> test_property_manager ... ok
> test_prosite ... ok
> test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
> test_seq ... ok
> test_translate ... ok
> test_trie ... ok
> test_triefind ... ok
> Bio.Seq docstring test ... ok
> Bio.SeqRecord docstring test ... ok
> Bio.SeqIO docstring test ... ok
> Bio.SeqIO.QualityIO docstring test ... ok
> Bio.SeqIO.AceIO docstring test ... ok
> Bio.SeqUtils docstring test ... ok
> Bio.Align.Generic docstring test ... ok
> Bio.AlignIO docstring test ... ok
> Bio.AlignIO.StockholmIO docstring test ... ok
> Bio.Application docstring test ... ok
> Bio.KEGG.Compound docstring test ... ok
> Bio.KEGG.Enzyme docstring test ... ok
> Bio.Wise docstring test ... ok
> Bio.Wise.psw docstring test ... ok
> Bio.Motif docstring test ... ok
> Bio.Statistics.lowess docstring test ... ok
> ======================================================================
> FAIL: Simple round-trip through app with clustal output
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "test_Mafft_tool.py", line 78, in test_Mafft_with_Clustalw_output
>     self.assert_(stdout.read().startswith("CLUSTAL format alignment by MAFFT"))
> AssertionError
> 
> ----------------------------------------------------------------------
> Ran 123 tests in 342.671 seconds
> 
> FAILED (failures = 1)
> #
> 
> So this time t_coffee test passed, sorry for the noise. I will try
> to find time next week to upgrade mafft. Thanks.

I've retitled the bug to focus on the MAFFT issue. This may well be
a problem with your old version of MAFFT - I know for example the
the FASTA output is broken on some versions of MAFFT.

Thanks,

Peter


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