48 lines
712 B
Plaintext
48 lines
712 B
Plaintext
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% Preliminary support for FASTA format.
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% Just convert sequence into string of atoms.
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%
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% support for a single sequence.
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%
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:- module(fasta, [fa2atoms/2,fa2atoms/3]).
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fa2atoms(F, L) :-
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fa2atoms(F, L, []).
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fa2atoms(F,L,L0) :-
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open(F,read,S),
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get0(S,C0),
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skip_header(C0,S),
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get0(S,C),
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read_chars(C, S, L, L0),
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close(S).
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read_chars(-1,_) --> [].
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read_chars(10,S) --> !,
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{ get0(S,MC) },
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read_chars(MC,S).
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read_chars(C,S) -->
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[AC],
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{
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cvt_c(C,AC),
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get0(S,MC)
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},
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read_chars(MC, S).
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cvt_c(C,A) :-
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C >= 0'A, C =< 0'Z, !,
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AC is C-(0'A-0'a),
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atom_codes(A,[AC]).
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cvt_c(C,A) :-
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C >= 0'a, C =< 0'z,
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atom_codes(A,[C]).
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skip_header(10,_) :- !.
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skip_header(_,S) :-
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get0(S,C),
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skip_header(C,S).
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