[Bioperl-guts-l] [Bug 2016] Bio::Align::metafasta

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Tue Jun 6 05:13:49 EDT 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2016





------- Comment #3 from bix at sendu.me.uk  2006-06-06 05:13 -------
(In reply to comment #2)
> adding two -- gap characters to the second sequence solves the exceptions but
> the tests don't pass, but again the expectations of the test could be wrong:

Well, to be more complete I should say that the test expects that everything in
the meta sequence is considered during consensus and symbol chars, but
SimpleAlign has no knowledge of Bio::Seq::Meta sequences and so ignores the
meta data. It's not completely trivial to add this knowledge, and I'd be more
comfortable doing it if I had more examples of metafasta files (especially some
real multiple alignments).


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