fasta.y
%{
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
int yylex();
int yyerror( char* message);
%}
%error-verbose
%token LT OTHER SYMBOL CR
%start input
%%
input: input sequence | optspaces sequence;
sequence: head body optspaces;
head: LT anylist CR | LT CR;
anylist: anylist any | any;
any: LT | OTHER | SYMBOL;
body: symbols CR | body symbols CR ;
symbols: symbols symbol | symbol ;
symbol: SYMBOL;
optspaces: | crlist;
crlist: crlist CR | CR;
%%
int yyerror( char* message)
{
fprintf(stderr,"NOT A FASTA %s\n",message);
exit(EXIT_FAILURE);
return -1;
}
int yylex()
{
int c=fgetc(stdin);
switch(c)
{
case EOF: return c;
case '>' : return LT;
case '\n' : return CR;
default: return isalpha(c)?SYMBOL:OTHER;
}
}
int main(int argc, char** argv)
{
return yyparse();
}
#compile
bison fasta.y
gcc -Wall -O3 fasta.tab.c
#test
$ ./a.out < ~/file.xml
NOT A FASTA syntax error, unexpected OTHER, expecting LT
$ ./a.out < ~/rotavirus.fasta
$