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

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2947





------- Comment #10 from pgarland at gmail.com  2011-02-04 23:23 EST -------
(In reply to comment #8)
> I'll volunteer to do all of that (OK with you, Phillip?).
> 
> Walter

Sure. WRT my earlier comment, I realized that it's simpler for both the
implementer and the user if the only user-visible change necessary to specify
begin states is to add a variable to HiddenMarkovBuilder to hold the name of
the begin state, and then let users use set_transition_score to specify
transition probabilities from begin states. Then the relevant methods, e.g.
_all_blank, allow_transition, allow_all_transitions, set_transition_score, etc
have to be altered to forbid transitions to, or emissions from the begin state.
And get_markov_model would raise an exception if a begin state hasn't been
specified or if there isn't at least one transition from the begin state. 

So all users would have to do is (using the example from the bug report):

...
build.begin_state_name = "begin"
build.set_transition_score("begin", "u", 0.01)
build.set_transition_score("begin", "f", 0.99)
...

~Phillip


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