[Biopython-dev] [Bug 2947] Bio.HMM calculates wrong viterbi path

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Feb 4 15:19:11 UTC 2011


------- Comment #8 from walter_gillett at hotmail.com  2011-02-04 10:19 EST -------
I'll volunteer to do all of that (OK with you, Phillip?).


(In reply to comment #6)
> (In reply to comment #5)
> > FWIW, I think the right thing with respect to begin states is to require the
> > user to explicitly specify an begin state in the state alphabet, e.g.:
> > class coin:
> >     def __init__(self):
> >         self.begin_state_name = "begin"
> >         self.letters = ["u", "f"]
> If we go that route, we'll need to make very clear the differences between a
> HMM Alphabet (of states) and a biological sequence alphabet (Bio.Alphabet). It
> must make sense in many cases to use a biological sequence alphabet, but in
> general adding HMM attributes to the class does not make sense.
> We really need someone to volunteer to take over this code (and sort out the
> overlap between Bio.MarkovModel and/or Bio.HMM.MarkovModel), write some
> documentation for the tutorial, and sort out these remaining issues. Are either
> of you interested?
> > 
> > I agree the variable names "main_state" and "cur_state" are confusing and
> > should be changed.
> > 
> I'll happily merge/cherry-pick a simple diff to do that only if you do that on
> github, or apply a patch if you upload it here.
> Thanks,
> Peter

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