[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 #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).

Peter


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