in reply to Base sequence length in fasta format file

As others have pointed out, this: my $base = ("A"|"C"|"G"|"T");doesn't do what you probably intended.

I'm not completely clear on what you're trying to do, but I think it's something like this: "if a line contains more than 250 bases, print it out" (where 250 can be changed easily). You don't need to count every single base: you can check that there's only A, T, C, or G in the line, and that it's longer than 250 characters. Something like this should do the trick (Note, this is untested):

while (<INPUT>) { print if /^[ATCG]+$/ && length >= $ideal; }
If the number of bases you're looking for is fixed, you can put it in the regular expression:     print if /^[ATCG]{250,}$/;But the first example I gave is probably clearer anyway.

If that's not the problem you're trying to solve, please provide more information.