Extremely Long String Help

[Gribouillis]

I suggest to convert the file externally by a C program for speed

#include<stdio.h>
#include<stdlib.h>
#include<ctype.h>
/* This is a C program */
int main()
{
      FILE *fp1, *fp2;
      char ch;
      fp1 = fopen("source.txt", "r");
      if (fp1 == NULL)
      {
            puts("Cannot open source.txt");
            exit(1);
      }
      fp2 = fopen("target.txt", "w");
      if (fp2 == NULL)
      {
            puts("Cannot open target.txt");
            fclose(fp1);
            exit(1);
      }
      while((ch=fgetc(fp1))!=EOF)
      {
          switch(ch){
              case 'a':
              case 'c':
              case 'g':
              case 't':
              case 'A':
              case 'C':
              case 'G':
              case 'T':
                ch = toupper(ch);
                fputc(ch,fp2);
          }
      }
      printf("File successfully converted.\n");
      return 0;
}

Edit: Actually, using fgetc() is much slower than using fread(). This can be improved a lot but on my computer it takes only 0.1 second for 10 MB..