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yap-6.3/packages/CLPBN/examples/HMMer/score.yap

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#!/usr/bin/yap -L --
#.
:- initialization(main).
:- ensure_loaded(library('clpbn/viterbi')).
:- use_module(fasta,
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[fa2atoms/3]).
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:- use_module(library(lists),
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[nth/3,
append/3
]).
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:- [plan7].
:- ['globin.yap'].
%:- ['hmmer_b.1.18.1.yap'].
:- dynamic len/1, emission/2.
main :-
unix(argv([Sequence])),
fa2atoms(Sequence, L, [a]),
run_model([a|L],_Trace).
artemia :-
fa2atoms('Artemia.fa', L, [a]),
run_model([a|L],_Trace).
% given a string, construct a model
run_model(String,Trace) :-
viterbi(s(0,_),t(_,_),String,Trace),
out(Trace,String).
write_keys([]).
write_keys([V|Vars0]) :-
clpbn:get_atts(V,[key(K)]), !,
write(K), nl,
write_keys(Vars0).
write_keys([_|Vars0]) :-
write(no_key),nl,
write_keys(Vars0).
convert2emissions([],_).
convert2emissions([E|String],I0) :-
I is I0+1,
assert(emission(I,E)),
convert2emissions(String, I).
out([],_).
out([State|Trace],String) :-
out_state(State,String,RString),
out(Trace,RString).
out_state(s(_),String,String).
out_state(n(_),[_|String],String).
out_state(j(_),[_|String],String).
out_state(c(_),[_|String],String).
out_state(t(_),String,String).
out_state(b(Pos),String,String) :-
format('START MATCH at ~d~n', [Pos]).
out_state(d(_,State),String,String) :-
find_consensus(State,Consensus),
format(' -~a~n', [Consensus]).
out_state(i(_,_),[Code|String],String) :-
to_upper(Code,UCode),
format(' ~a+~n', [UCode]).
out_state(m(_,State),[Code|String],String) :-
to_upper(Code,UCode),
find_consensus(State,Consensus),
find_match_type(State,Code,Consensus,MatchType),
format(' ~a~a~a~n', [UCode,MatchType,Consensus]).
out_state(e(Pos),String,String) :-
format('END MATCH at ~d~n', [Pos]).
to_upper(A,U) :-
atom_codes(A,[C]),
( C =< "A", C>="Z" ->
U = A
;
NC is C + ("A"-"a"),
atom_codes(U,[NC])
).
find_consensus(State,Consensus) :-
consensus(State,I),
hmm_domain(Type),
domain_vals(Type,Vals),
arg(I, Vals, Consensus).
find_match_type(_,Code,Code,'=') :- !.
find_match_type(State,Code,_,'^') :-
me_cpt(State,Probs,_,_),
hmm_domain(Type),
domain_vals(Type,Vals),
find_prob_for_code(Vals,Code,Probs,Prob),
Prob >= 0, !.
find_match_type(_,_,_,' ').
find_prob_for_code(Vals,Code,Probs,Prob) :-
Vals =.. [_|L],
once(nth(I,L,Code)),
arg(I,Probs,Prob).
domain_vals(aminoacids,domain(a, c, d, e, f, g, h, i, k, l, m, n, p, q, r, s, t, v, w, y)).
domain_vals(bool,domain(t,f)).
domain_vals(bases,domain(a,c,g,t)).
domain_vals([A|B],Domain) :-
Domain =.. [domain,A|B].
start(S) :-
s_state(0,S).
end(Items,E) :-
t_state(Items,E).