[Biopython-dev] [Bug 3042] test_Mafft_tool fails

[Cymon Cox]

On 6 April 2010 07:14, <bugzilla-daemon at portal.open-bio.org> wrote:

> http://bugzilla.open-bio.org/show_bug.cgi?id=3042
>
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> ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2010-04-06 02:14 EST -------
> (In reply to comment #0)
> > This is with MAFFT version 5.732 (2005/09/14). The output it generates
> starts
> > with:
> > ...
> > 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.
>
> I think you are right this is due to your version of MAFFT. The lattest
> version is MAFFT 6.717, the first public 6.x release was back in 2007.
> MAFFT 5.732 from late 2005 is really *very* old, right at the bottom of
> the release history page:
> http://mafft.cbrc.jp/alignment/software/changelog.html
>
> Probably the best solution here is to detect the version number (perhaps by
> the date?), and skip the tests if it is too old (like test_Emboss.py does
> now).
>


For the alignment tool interfaces we could only test against the versions
that the wrappers were written against (Mafft was  6.626b for instance), and
skip all other versions - but that may be a bit drastic. Perhaps detecting
the version and issuing a warning such as "This test may have failed because
you are using an older/newer version of X", if necessary, is more
appropriate.

I'll look again at newer versions of these alignment tools (when I get a
chance...).

Cheers, C.
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