This repository has been archived on 2023-08-20. You can view files and clone it, but cannot push or open issues or pull requests.
yap-6.3/packages/CLPBN/examples/HMMer/fasta.yap
2012-12-19 18:22:47 +00:00

50 lines
721 B
Prolog

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