48 lines
712 B
Prolog
48 lines
712 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).
|
|
|
|
|
|
|