[Biopython-dev] [Bug 2542] AlignInfo.py fails a test

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2542





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-11 05:50 EST -------
I think I've fixed the "Quick test" failure when running Bio/Align/AlignInfo.py
directly.  I don't know how I missed that before...

/home/repository/biopython/biopython/Bio/Align/AlignInfo.py,v  <-- 
AlignInfo.py
new revision: 1.15; previous revision: 1.14
done

My opinion from from looking at the AlignInfo code, and scanning back over the
CVS history, is that it was ever used much with generic alphabets (as tend to
be returned by Bio.AlignIO).  There may be other issues here - for example I've
spotted another problem case, doubly extended alphabets like a protein alphabet
with declared Gapped and WithStopCodon (which you *might* want in an
alignment).


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