[Bioperl-l] t/SimpleAlign: not ok 18

[Allen Smith]

On Sep 16,  4:53pm, Allen Smith wrote:
> On Sep 12,  8:05am, Jason Stajich wrote:
> > I cannot replicate on either the released tarball or current 1-0-0 branch
> > on IRIX with perl 5.6.1.  Very strange.  Can it be a 5.8.0 bug?  That
> > seems odd but possible.
> 
> Well, I just took a look at SimpleAlign's consensus procedure, and I can see 
> why there's a difference - and it is a _bioperl_ bug, not a perl bug. Perl
> 5.8.0 uses a different hash algorithm, resulting in having a different
> ordering of letters with "each". The alignment in question has equal numbers 
> of 'D's and 'E's at the third position. Previously, the ordering of the hash 
> resulted in 'D' coming first; it now results in 'E' coming first.

[...]

> This is, however, not what I would describe as an ideal fix. I suggest that
> taking into account what the other residues are (if doing a protein
> consensus) and which one of the two (or more) tied residues they are most
> similar to would be preferable (using the CONSERVATION_GROUPS rules for
> which is most similar, probably, although allowing user modification of this 
> is desirable).

BTW, Chris, I am pleased to see bioperl back online - thanks for your
efforts, especially with your having been in Singapore!

Well, I've been looking at doing the above - using bioperl-1.1.0 from a
mirror site, since CVS was inaccessible (I've now downloaded bioperl-live
HEAD). I'm currently looking at consensus et al stuff in SimpleAlign with a
view toward enabling a loose consensus mechanism, with that also being used
for tiebreaking in ties for strict consensus situations. This would be via
matrices, which is leading me into splitting out the matrix code in
Bio::Variation::AAChange and SimpleAlign (CONSERVATION_GROUPS) into a
seperate Bio::Matrix (and Bio::MatrixI) module. Thoughts?

	-Allen

-- 
Allen Smith			http://cesario.rutgers.edu/easmith/
September 11, 2001		A Day That Shall Live In Infamy II
"They that can give up essential liberty to obtain a little temporary
safety deserve neither liberty nor safety." - Benjamin Franklin