[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 #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-05-07 04:49 EST -------
(In reply to comment #3)
> 
> This is the output I am now getting:
> 
> ======================================================================
> FAIL: Round-trip with complex command line.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "test_Mafft_tool.py", line 144, in test_Mafft_with_complex_command_line
>     % (return_code, cmdline))
> AssertionError: Got error code 1 back from:
> mafft --localpair --weighti 4.2 --retree 5 --maxiterate 200 --nofft --op 2.04
> --
> ep 0.51 --lop 0.233 --lep 0.2 --reorder --treeout --nuc Fasta/f002
> 
> If I just run this mafft command directly, I get:
> 
> $ mafft --localpair --weighti 4.2 --retree 5 --maxiterate 200 --nofft --op 2.04
> --ep 0.51 --lop 0.233 --lep 0.2 --reorder --treeout --nuc Fasta/f002
> /usr/local/bin/mafft: line 184: [: --treeout: integer expression expected
> Unknown option:  --treeout
> 
> MAFFT version 5.732 (2005/09/14)
> ...

It looks to me like some of the other arguments the test is trying to use are
also not supported on this version of MAFFT.

> > 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.
> > 
> 
> This is the output of "mafft --help":
> 
> $ mafft --help
> Cannot open --help.
> 
> MAFFT version 5.732 (2005/09/14)
> ...

Great. That's enough to be able to detect the version number.

Note that MAFFT v6 doesn't support the --help argument, the point is it will
abort with help text and not sit waiting on stdin.

I've update the unit test to require MAFFT v6 or later, which should resolve
this bug.
http://github.com/biopython/biopython/commit/e2219beb156e80b55da3efb4a8efe2c2347ec877

Thanks for your help,

Peter


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